Portsmouth have confirmed that executive director Velimir Zajec has resigned for personal reasons.
"I am very sad to lose services of Velimir, but we must respect his personal reasons," chairman Milan Mandaric told the club website.
"He joined the club last year and stepped into the breach as temporary manager when Harry Redknapp left.
"He took us through a difficult period before Alain Perrin joined us and I would like to thank him."
Portsmouth have insisted there would be no rush to replace Zajec.
Pompey chief executive Peter Storrie said: "It is a sad day for the club. Velimir was doing a good job but he has his reasons for leaving.
"There will be no hurry to name a replacement and we will wait and see how things settle down."
Zajec's appointment as executive director by Mandaric was controversial from the moment the former Panathinaikos boss arrived at Fratton Park.
His brief was to scout for players and to improve Pompey's football infrastructure.
Then Pompey boss Redknapp quit not long after Zajec's arrival.
Zajec was asked to take over the reins but was never entirely comfortable in the role.
Israeli midfielder Eyal Berkovic claimed that Zajec was the reason he left the club, while keeper Shaka Hislop claimed he was frozen out.
Zajec returned to the background after helping recruit his successor, current boss Alain Perrin.
But he is believed to have become frustrated with his role at Fratton Park, with his requirement to scout for players and his attempts to set up an academy, which were hampered by a tightening of purse strings by Mandaric.
However, Zajec told the club website he was very sad to be leaving the club and asked the media to respect his privacy over his decision to leave.
"These are very personal reasons and I wish them to remain that way," he said.
"I have enjoyed my time at the club, where I have made many friends. Portsmouth is a special club and I leave wishing them every success for the future."