The National Security Agency's top civilian employee is leaving abruptly, as the agency continues to be swept by turmoil over its controversial surveillance powers.

John Inglis, who has spent nearly eight years as the deputy director of the NSA, is retiring weeks after Washington speculation placed him as a top candidate to be the first civilian to run the agency.

Inglis’ departure, first reported by Reuters and Foreign Policy magazine and independently confirmed by the Guardian, is set for the end of the year. In a few months he will be joined by his boss, US army General Keith Alexander, who is also stepping down after eight years. The moves give President Barack Obama an opportunity to reshape the leadership of a spy agency that has sparked one of the most intense diplomatic crises of his presidency.

The NSA said on Friday that Inglis’ imminent retirement was part of a long-scheduled transition and was not indicative of further departures.

“The plan has been set for some time, first announced internally at NSA this past summer, for Mr Inglis to retire at year’s end and [General] Alexander in the spring of 2014. In each case, their time in office represented a significant extension of service beyond their original tours,” said an NSA spokeswoman, Vanee Vines.

“Consistent with that plan, Mr Inglis stepped down this week to start the transition process. Ms Fran Fleisch is currently serving as the acting deputy director, pending administration concurrence in Mr Inglis’ long-term successor.”

That successor is rumored to be Rick Ledgett, an NSA civilian currently leading the agency’s internal review into the extent of the alleged damage caused by the whistleblower Edward Snowden. Vines said she had no comment about the “speculation” that Ledgett will take the agency’s second-highest job.

Inglis' departure comes as speculation runs high about potential changes to the NSA. On Sunday, Obama is slated to receive the report of an advisory committee he created in August to advise him on surveillance reforms, although early leaks indicate it will recommend more continuity than change.

Inglis had recently been cited in media reports as a leading candidate to become the NSA’s first civilian leader. That prospect all but died on Friday as the White House said it had decided, over the wishes of its surveillance review panel, to keep the NSA director as the same person who runs the military’s new Cyber Command, a position for a four-star general or admiral.

Beyond unilateral changes, privacy advocates in the House and Senate have sponsored a bill to end the bulk collection of all Americans’ phone data, the most politically controversial of the NSA’s vast intelligence powers. While supporters claim the bill has 120 co-sponsors, it has no chance of passing until at least the new year. Obama, who has pledged to get the “balance” between civil liberties and national security right, has yet to take a position on the bill.

Inglis has been a prominent figure since the Snowden disclosures forced the NSA into the spotlight. He has testified in front of Capitol Hill committees more often than Alexander has, making the case to both supportive and hostile legislators that the agency's bulk surveillance programs – including those that collect Americans’ phone data – are both legal and reasonable.

More recently, Inglis has taken his case outside of the Beltway as part of a new push to rally public confidence in the agency, even as he has conceded that some restrictions on NSA powers are inevitable. In November Inglis gave a wide-ranging talk at the University of Pennsylvania Law School, in which he invited a student critic of the NSA to become a civil liberties officer at the agency.

Ledgett, Inglis’s rumored replacement, told CBS for an interview scheduled to air Sunday on 60 Minutes that he was open to a deal to provide amnesty to Snowden, bringing him back to the US from Russia, in exchange for the return of all of the data Snowden took from the agency.

“I would need assurances that the remainder of the data could be secured, and my bar for those assurances would be very high,” Ledgett was quoted as saying. Alexander has publicly said that an amnesty for Snowden would be a mistake.

It is difficult to know how Snowden could provide such assurances. He told the New York Times in October that he did not take any of his surveillance documents to Russia, where he has received a year-long temporary asylum.

Inglis did not immediately return a request for comment.