GOP Accuses State Dept. of 'Cover-Up' to Protect Hillary Clinton Over Emails State under pressure to explain what happened to emails of Clinton IT staffer.

 -- The Republican Party is accusing the State Department of “stonewalling” a request to obtain the missing emails belonging to an information technology staffer who helped maintain Hillary Clinton’s private server, suggesting the delay is part of a “cover-up to protect” the Democratic presidential nominee.

New documents, first seen by ABC News, show that the State Department has not responded to a months-old request from the National Archives and Records Administration (NARA) to explain why it has so few email records belonging to the senior staffer, Bryan Pagliano, who worked at the department as a political appointee from May 2009 to February 2013.

During the course of Clinton’s email imbroglio, Pagliano developed a reputation as quiet insider with knowledge of Clinton’s controversial email configuration. He signed an immunity agreement with the Justice Department in exchange for cooperating with FBI investigators examining Clinton’s use of that private email server and has invoked his Fifth Amendment rights hundreds of times in response congressional and legal inquiries. In May, the State Department announced it couldn’t find any evidence that Pagliano had turned over his emails prior to leaving the department, which he would have been required by law to do.

According to the new documents obtained by the Republican National Committee (RNC) through freedom of information requests and shared with ABC News, NARA asked the State Department on July 18 to provide a report within 30 days explaining why it’s been unable to produce Pagliano’s emails. Three months later, however, the State Department has yet to respond.

In its letter to the State Department’s records office, NARA also said “if it’s determined Federal records have been alienated or destroyed, please describe all measures your agency has taken, or expects to take, to retrieve the alienated records or retrieve them, to the extent necessary and appropriate.”

RNC Chairman Reince Priebus says the subsequent delay amounts to stonewalling.

“The State Department is clearly stonewalling another federal agency’s efforts to recover the emails of the IT staffer who set up Clinton’s illegal server and was granted immunity by the FBI," Priebus told ABC News. "If this isn’t an Obama Administration cover-up to protect Hillary Clinton, I don’t know what is.”

The State Department adamantly denied the RNC's accusations.

"There is no stonewalling and there is no cover-up," State Department spokesman John Kirby said in a statement to ABC News, adding that the department plans to respond to NARA's letter.

"As we have publicly explained months ago, the Department has searched for Mr. Pagliano’s email pst file and has not located one that covers the time period of Secretary Clinton’s tenure," Kirby said, referencing a file type that would have held Pagliano's emails.

Kirby, however, did not offer a reason for missing the deadline or an explanation of what efforts the department has taken to retrieve the emails.

"As we have also previously explained, employees’ emails have not always been automatically retained, so the absence of this email file does not necessarily indicate that Mr. Pagliano intentionally deleted his emails," Kirby said.

Kirby defended the State Department's efforts, saying that although Pagliano didn't turn any emails over before leaving, some of his email was captured and retrieved via separate government accounts. State Department officials added that "hundreds of pages" of those recovered emails have been shared with Congress and the RNC, which acquired them through a freedom of information lawsuit.

In his statement, Kirby also says that Pagliano did provide a file of his emails when he worked more recently as a contractor for the State Department but by that time, Clinton had left office.

The RNC told ABC News that NARA could request that the U.S. attorney general initiate action to recover those emails and that any such investigation into what happened to those emails could be problematic for Pagliano -- assuming he deleted the records, as the RNC believes. Penalty for unlawful or accidental removal or destruction of records can include a fine, imprisonment or both.

Although the details of Pagliano's immunity agreement with the Justice Department aren't publicly known, the RNC believes it's unlikely the agreement would protect him from potential prosecution for the alleged destruction of federal records.

The RNC also believes Pagliano should have known about his duty to retain federal records, including his own. The FBI's final investigative report on Clinton's email cites interviews it conducted with Pagliano. In them, Pagliano recounts how he was told in late 2009 or early 2010 by an official (whose name is withheld) that Clinton's server "may be a federal records retention issue." Pagliano also told the FBI that he relayed those concerns to two other top officials in Clinton's inner circle.

In the meantime, the State Department says it is working to improve its records management systems and that it is now automatically archiving current Secretary of State John Kerry's emails as well as the emails of numerous senior staffers.