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In a rare public order, the secretive Foreign Intelligence Surveillance Court responded to problems with the eavesdropping on a former Trump campaign aide uncovered by an inspector general.

A secretive federal court accused the F.B.I. on Tuesday of misleading judges about the rationale for wiretapping a former Trump campaign adviser and ordered the bureau to propose changes in how investigators seek their permission for national security surveillance targeting Americans.

In an extraordinary public order, the presiding judge on the Foreign Intelligence Surveillance Court, Rosemary M. Collyer, gave the F.B.I. a Jan. 10 deadline to come up with a proposal. It was the first public response from the court to the scathing findings released last week by the Justice Department’s independent inspector general about the wiretapping of the former Trump adviser, Carter Page, as part of the Russia investigation.

“The frequency with which representations made by F.B.I. personnel turned out to be unsupported or contradicted by information in their possession, and with which they withheld information detrimental to their case, calls into question whether information contained in other F.B.I. applications is reliable,” Judge Collyer wrote.

The court “expects the government to provide complete and accurate information in every filing,” she added, using italics to emphasize the court’s anger.

While the inspector general, Michael E. Horowitz, debunked the claims by President Trump and his allies that senior F.B.I. officials were part of a political conspiracy, his investigation also exposed a litany of errors and inaccuracies where case agents cherry-picked the evidence about Mr. Page as they sought permission to eavesdrop on his calls and emails.

The F.B.I. issued a statement noting that its director, Christopher A. Wray, had called the conduct by certain employees described in the report “unacceptable and unrepresentative of the F.B.I. as an institution” and ordered “more than 40 corrective steps” to address the problems found by the inspector general.

At a Senate Judiciary Committee hearing last week about the report’s findings, the chairman of the panel, Senator Lindsey Graham, Republican of South Carolina, addressed the court that oversees wiretapping under the Foreign Intelligence Surveillance Act, or FISA, telling the judges that they needed to take steps to preserve political support for the national security surveillance system.

“The FISA system, to survive, has to be reformed,” Mr. Graham said. “To the FISA court: We’re looking to you to take corrective action. If you take corrective action, that will give us some confidence that you should stick around. If you don’t, it’s going to be hurtful to the future of the court, and I think all of us are now thinking differently about checks and balances in that regard.”

The inspector general’s findings have also fueled renewed criticism by privacy advocates about the pervasive secrecy that generally permits the government to make one-sided presentations to the FISA court without the prospect of challenges by outsiders, even later on when investigations have ended. The FISA court has long been criticized for its secrecy.
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Mr. Horowitz is scheduled to testify about the report again on Wednesday at a hearing before the Senate Homeland Security and Governmental Affairs Committee.

Mr. Horowitz suggested several changes. He recommended that the F.B.I. overhaul its FISA paperwork to ensure that it identifies any information that might reduce suspicions about a target; surface any reasons to be skeptical about an informant whose information is used to apply for a court order for a wiretap; and require agents and supervisors to reverify factual assertions that they use to pursue renewed permission for wiretaps.

Mr. Wray has said he accepted Mr. Horowitz’s findings and embraced the need to make changes. He said last week that he was ordering “concrete changes” to ensure that the FISA process was “more stringent and less susceptible to mistake or inaccuracy.”

Among other ideas floated by proponents of overhaul, including the American Civil Liberties Union: appointing a third party to critique the government’s cases for wiretapping people, at least in sensitive investigations, or allowing defense lawyers with security clearances to see the government’s evidence presented to the FISA court on those rare occasions when it is used to prosecute a suspect.

Mr. Horowitz has already begun an audit of other FISA applications to see whether a broader pattern of problems exists in how the F.B.I. portrays for the court its evidence about suspects whom agents want to wiretap. Another possibility for overhaul is that going forward, the bureau’s general counsel could oversee recurring audits of a random sampling of FISA applications, so that case agents will always have to take into account that someone may later second-guess their work.

In his report, Mr. Horowitz scrutinized the four applications that the Justice Department submitted from October 2016 to June 2017 to wiretap Mr. Page, whom F.B.I. agents suspected might be a conduit between the Trump campaign and Russia during its covert operation to manipulate the 2016 presidential election.

The review uncovered a deeply dysfunctional and flawed process riddled with inaccuracies and material omissions. Investigators highlighted facts that made Mr. Page look suspicious while letting potentially exculpatory ones go unmentioned, and when they sought to renew the wiretap, they failed to correct earlier statements whose credibility had since come under serious question, the report found.

Justice Department lawyers who deal directly with the FISA court passed that misleading portrait onto the judges. While Mr. Horowitz’s findings placed most of the direct blame on a handful of case agents and their supervisors who worked directly with the raw evidence,  his report also said senior officials bore responsibility for permitting systemic failures to fester.

Mr. Horowitz’s investigators found no evidence that political bias against Mr. Trump was behind the problems — as opposed to apolitical confirmation bias, gross incompetence or negligence. But the inspector general said the explanation the F.B.I. offered — that the agents had been busy with other aspects of the Russia investigation, and the Page FISA was a minor part of those responsibilities — was unsatisfactory.

Congress enacted FISA in 1978 to regulate the government’s use of domestic surveillance for national security investigations — those aimed at monitoring suspected spies and terrorists — as opposed to ordinary criminal cases. The law sets up a special court, made up of 11 sitting district court judges who are selected to serve staggered terms by the chief justice of the Supreme Court, and decide whether the evidence shows a target is probably a foreign agent.

Judge Collyer, who was appointed a federal district judge in Washington by President George W. Bush, has presided over the surveillance court since 2016. The chief justice of the Supreme Court, John G. Roberts Jr., had tapped her for a seat on it three years earlier, just before the disclosures by the former intelligence contractor Edward J. Snowden set off a wide debate over surveillance and privacy.

In 2018, government records show, the court fully denied only one of 1,080 final applications submitted under FISA to conduct electronic surveillance. However, the court also demanded unspecified modifications to 119 of those applications before approving them. There were 1,833 targets of FISA orders, including 232 Americans, that year.

National security wiretaps are more secretive than ordinary criminal ones. When criminal wiretap orders end, their targets are usually notified that their privacy has been invaded. But the targets of FISA orders are usually not told that their phone calls and emails have been monitored, or that their homes or businesses have been searched.

And when people are prosecuted for crimes based on evidence derived from ordinary criminal wiretaps, the defendants and their lawyers are usually allowed to see what the government told judges about them to win approval for that surveillance, giving them the opportunity to argue that investigators made mistakes and the evidence should be suppressed.

But defense lawyers, even those with security clearances, are not shown FISA applications for their clients. As a result, there is no prospect of second-guessing in an adversarial court setting to keep F.B.I. agents scrupulous about how they portray the evidence when seeking to persuade FISA judges to sign off on putting a target under surveillance.

In the absence of that disciplining factor, the Justice Department and F.B.I. have developed internal procedures that are supposed to make sure that the evidence presented in FISA applications is accurate and includes any facts that might undercut the government’s case. But that system failed in the Page wiretaps, Mr. Horowitz’s report showed.

At the Senate hearing, one of the rare areas of agreement between Republicans and Democrats was the need for change to the FISA system. Senator Richard Blumenthal, Democrat of Connecticut, who has unsuccessfully proposed legislation to tighten restrictions on national-security surveillance in the past, said he welcomed the moment.

“I hope my Republican colleagues who have been so vocal and vehement about the dangers of potential FISA abuses will join me in looking forward and reform of that court,” Mr. Blumenthal said, adding, “I hope that we can come together on a bipartisan basis to reform the FISA process.”