It was set up as a unique historical experiment: an agency that would open up the secret service's files to those it had spied upon. But now the commissioner in charge of the East Germany's secret police archive has admitted that his agency still counts 37 former Stasi employees among its staff.

The Federal Commission for the Stasi Archives was established by the German government in 1991 and tasked with protecting the Stasi archives from former agents eager to destroy records of their deeds, as well as allowing access to anyone with a reasonable suspicion that they may have been watched over by the state.

In 2007, a leaked German government report revealed that the archive had since its inception employed as many as 79 former Stasi members, some of them without the knowledge of parliament, fuelling suspicions that incriminating files could have been destroyed or been tempered with.

In his inaugural speech in March 2011, the current commissioner, Roland Jahn, a former dissident journalist, had described it as "intolerable" that Stasi victims seeking access to their files would have to deal with former employees of the secret police. "Every former Stasi collaborator who is still employed by the agency," he said, "is a slap in the victims' faces."

But on Friday it emerged that the archive still employs 37 workers who have previously worked for the Stasi among its 1,600 staff members. In an interview with Tagesspiegel newspaper, Jahn admitted that resolving the issue had proved harder than anticipated. Under German employment law, public servants can only be moved on to "comparable" posts in other agencies.

"There are still 37 of them here. Five [out of 48 he had to deal with originally] have been moved on, five have left for age reasons, and one of them has died. All other transfers are on the way. But many employees say: no way am I moving on. And so the whole affair is delayed."

By the time of its collapse, the Stasi is estimated to have had 91,000 full-time employees and between 110,000 and 190,000 informants. While it is likely many of those re-hired by the government agency were mere technicians or archival clerks, at least two were high-ranking officers.

The latest revelations also throw up uncomfortable questions for the German president, Joachim Gauck, who was the inaugural commissioner for the Stasi archives between 1990 and 2000. In his 1991 book The Stasi Files, Gauck had defended re-hiring old Stasi personnel: "We couldn't have done without their specialist knowledge of certain branches and the Stasi's archiving system." Originally hired on short-term contracts, Gauck had personally lobbied to make their jobs permanent in 1997.

Klaus Schroeder, a historian at Berlin's Free University who looked into the deployment of Stasi at the agency in 2007, told the Guardian: "Ultimately, the responsibility for giving these people uncontrolled access to high-profile files lies with Gauck."

Jahn, the current commissioner, also used his interview in Tagesspiegel to dismisses comparisons between the US National Security Agency and the Stasi: "I find it absurd to equate the NSA and the Stasi – it's a smokescreen. It doesn't help us in clearing up the current intelligence scandals, and it trivialises the work of the Stasi. They didn't just gather information but also lock up those who criticised the state. But the NSA debate has shown how important it is to raise your voice when basic human rights are being violated."