Department of Justice officials apologized in court filings made public Thursday for failing to inform the Foreign Intelligence Surveillance Court of preservation of evidence orders against the National Security Agency.

Judge Reggie Walton, presiding judge of the FISC, ordered the apology and explanation March 21, setting a Wednesday due date, after government attorneys failed to notify him of preservation of evidence orders given to the Electronic Frontier Foundation in a case against the NSA’s bulk phone record collection.

The omission caused Walton to issue an erroneous March 7 ruling, in which he denied a government request to store phone records longer than five years.

In that ruling, Walton said government attorneys’ fear of penalties if they deleted the older records was “far-fetched as the plaintiffs [in six pending anti-surveillance cases] appear not to have made any attempt to have the [bulk] metadata retained.”

The EFF – which filed lawsuits in 2008 and 2013 against the NSA's phone record collection – quickly pointed out that Walton was misinformed.

“On February 26, 2014, movants contacted the Government and called to its attention its failure to inform this Court of the existing preservation orders. To movants’ knowledge, the Government did not attempt to correct the record before this court,” EFF attorney Kurt Opsahl wrote in a March 8 filing.

Walton had to reverse himself, deferring to lower court rulings on preservation of evidence after U. S. District Court Judge Jeffrey White of San Francisco granted a temporary restraining order blocking the NSA from destroying older records. White is evaluating the preservation order dispute.

“With the benefit of hindsight, the Government recognizes that upon receipt of plaintiffs’ counsel’s e-mail, it should have made this Court aware of those preservation orders,” Assistant Attorneys General John Carlin and Stuart Delery said in a filing submitted Wednesday and publicly released Thursday.

The filing said the government believed the preservation of evidence orders cited by EFF were not relevant.

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“The Government sincerely regrets not having brought these matters to the Court’s attention prior to its March 7, 2014, ruling and assures the Court that it will apply utmost attention to its submissions in this and all other matters before this Court,” Carlin and Delery wrote.

In a separate filing submitted Thursday, Department of Justice officials apologized again, this time for a minor inaccuracy in the Wednesday apology.

“It has come to the attention of the Government that footnote 6 on page 5 [of the apology] is not accurate as written,” they wrote. “The Government apologizes for the error.”

Opsahl, the EFF attorney, tells U.S. News the apology “illustrates the failures of the FISC's one-sided court system.”

“As it admits, the government unilaterally decided that it was right about its interpretation of the [pending] case, and therefore did not tell the court about the disagreement,” Opsahl says. “This elevates the DOJ attorneys into a role of a judge, with no accountability except in the rare circumstance like this.”

Opsahl also takes issue with the apology, saying the government attorneys further misled the court.

The apology calls EFF’s claim that the preservation orders are relevant "recently-expressed views," with which Opsahl disagrees.

“DOJ uses this notice to present that disagreement over the scope of the cases with only the government's spin, failing to mention the various arguments we made on that issue before Judge White,” Opsahl says. “DOJ does not mention to the FISC that we wrote in a 2010 brief that the ‘government defendants’ assertion that 'plaintiffs do not challenge surveillance authorized by the FISA Court' … misconceives both plaintiffs’ complaint and the role of the district court.’”