FBI Director Robert Mueller struggled to stop subordinates from criticizing the NYPD over its case against accused would-be pipe-bomber Jose Pimentel, he admitted Wednesday.

The feds passed on the case twice, but the NYPD took down the Bronx radical as he worked to complete a pipe bomb in a police informant’s apartment on Nov. 20.

Afterward, federal officials ripped the case, telling reporters, who gave them anonymity so they could dish, that Pimentel was incapable of carrying out an attack.

U.S. Sen. Chuck Grassley (R-Iowa) took Mueller to task before the Senate Judiciary Committee Wednesday, telling him that “FBI agents should not anonymously or publicly attack the New York Police Department.”

Mueller agreed, but said it took some work to silence the muttering.

“I gave directions that that should not happen, and when I saw it happening again, went back to give directions to have it stopped,” Mueller said.

Mueller had his deputy reach out to NYPD Commissioner Raymond Kelly, who phoned Mueller to talk things over, the FBI boss said.

“Ray Kelly has done a remarkable job in terms of protecting New York City from terrorist attacks, New York City being a principal target,” Mueller said.

“These things are unfortunate, I wish they didn’t happen, but our relationship remains solid.”

NYPD Deputy Commissioner Paul Browne confirmed that Mueller and Kelly discussed the issue.

“Director Mueller has consistently supported the NYPD’s efforts, and his remarks today were appreciated as well,” Browne, the NYPD’s top spokesman, said Wednesday.

Grassley reminded Mueller that his agency has a reputation for “not playing well with others.”

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