The FBI refused to cooperate Monday with a court-ordered inquiry into former Secretary of State Hillary Rodham Clinton’s email server, telling the State Department that they won’t even confirm they are investigating the matter themselves, much less willing to tell the rest of the government what’s going on.

Judge Emmet G. Sullivan had ordered the State Department to talk with the FBI and see what sort of information could be recovered from Mrs. Clinton’s email server, which her lawyer has said she turned over to the Justice Department over the summer.

The FBI’s refusal, however, leaves things muddled.

“At this time, consistent with long-standing Department of Justice and FBI policy, we can neither confirm nor deny the existence of any ongoing investigation, nor are we in a position to provide additional information at this time,” FBI General Counsel James A. Baker wrote in a letter dated Monday — a week after the deadline the Justice Department had set for the FBI to reply.

Judicial Watch, a conservative public interest law firm that is pursuing at least 16 open records cases seeking emails from Mrs. Clinton and her top aides, said at this point it’s not even clear what Mrs. Clinton provided, since all that’s been made public at this point are the former secretary of state’s public comments and some assertions, made through her lawyer, to the State Department.

Judicial Watch is prodding the courts to try to delve more deeply into Mrs. Clinton’s emails, and the group said a number of questions persevere about both Mrs. Clinton and top aides such as Huma Abedin, who did public business on an account tied to the server Mrs. Clinton maintained.

“We still do not know whether the FBI — or any other government agency for that matter — has possession of the email server that was used by Mrs. Clinton and Ms. Abedin to conduct official government business during their four years of employment at the State Department,” Judicial Watch said.

“We also do not know whether the server purportedly in the possession of the FBI — an assumption based on unsworn statements by third parties — is the actual email server that was used by Mrs. Clinton and Ms. Abedin to conduct official government business during their four years of employment at the State Department or whether it is a copy of such an email server. Nor do we know whether any copies of the email server or copies of the records from the email server exist,” the group said in its own court filing Monday afternoon.

Judicial Watch did release more than 50 pages Monday of emails it obtained from Ms. Abedin’s account on Mrs. Clinton’s server, and said it was clear she was talking about “sensitive” topics that shouldn’t have been discussed on an insecure account.

Many of those were details of Mrs. Clinton’s movements overseas, such as hotels she was staying at.

“These emails Judicial Watch forced out through a federal lawsuit show that Huma Abedin used her separate clintonemail.com account to conduct the most sensitive government business, endangering not only her safety but the safety of Hillary Clinton and countless others,” said Judicial Watch President Tom Fitton.

He questioned what reason Ms. Abedin — who did maintain an account, [email protected], on State.gov servers — would have for using the other account for important business. Mrs. Clinton said she kept only one account, the one on the clintonemail.com server, because it was more convenient, but that reasoning does not appear to apply to Ms. Abedin.

The State Department is making all of Mrs. Clinton’s emails public under order of Judge Rudolph Contreras. But the department has said it won’t make all of the emails public from Ms. Abedin or other top Clinton aides Cheryl Mills or Philippe Reines. Instead the department only plans to release those messages specifically requested in open records demands.

Mrs. Clinton turned over about 30,000 email messages in December, while her aides turned over more than 100,000 pages between them, with the final set only being returned, by Ms. Abedin, earlier this month, the department said in court filings.

Without those documents in hand, the State Department has been unable to do full and complete searches in response to subpoenas, congressional inquiries or Freedom of Information Act requests.

The State Department has asked for dozens of cases to be put on hold while it tries to get a single judge to coordinate all of its searches in more than two dozen cases. But the people requesting the records have objected, and say the State Department has nobody to blame but itself.

“The State Department acts as if Ms. Abedin’s and Ms. Mills’ documents fell from the sky on the eve of the State Department’s production deadline, but that is not remotely the case,” Citizens United, one of the plaintiffs who has sued under the FOIA, said in a filing late last week.

Citizens United says the State Department missed its own deadline for producing Ms. Mills’ and Ms. Abedin’s documents.

The Obama administration countered that it went above and beyond its duties under the law by asking Ms. Abedin and Ms. Mills to return their records and then to search them in response to open records requests. The State Department says it’s moving as quickly as possible, but says the sheer number of documents — and the number of requests for them — calls for a stay in most cases.

But of the 26 requests where the State Department has sought to halt proceedings, six have already been denied. Only one has been granted, one was granted in part and denied in part by the same judge, and another is being held in abeyance.

The State Department told one of the federal judges Monday that it’s facing nearly 100 different open records lawsuits — not all of them related to Mrs. Clinton’s email server — that have stretched officials to their limit.

Monday’s FBI letter underscores the tangled situation Mrs. Clinton’s emails have produced. The letter was addressed to Mary McLeod, a lawyer at the Justice Department, which oversees the FBI — and which means, in effect, that the FBI is refusing to talk to its own parent department about the matter.

Mr. Baker pointedly noted in his letter that he was aware the response would be submitted to the court, which would presumably make it public.

Earlier this month the Justice Department, in another pleading, insisted Mrs. Clinton didn’t do anything wrong in being the one who decided which of her messages were official business records that must be returned to the government and which were purely personal and able to be expunged.

Judicial Watch said that raises thorny questions for a department that is supposedly investigating Mrs. Clinton.

Last week Sen. John Cornyn, the second-ranking Republican in the Senate, called for Attorney General Loretta E. Lynch to name a special counsel to oversee the investigation, citing too many potential conflicts of interest.

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