Sir Kenneth Bloomfield, the UK commissioner for the Independent Commission for the Location of Victims’ Remains (ICLVR), is to step down.
The commission was established in 1999 to help locate those abducted, murdered and secretly buried by the IRA during the Troubles.
The independent body set up in 1999 after the Good Friday peace agreement liaises with former paramilitaries to find 16 victims clandestinely buried.
Among the bodies to have been recovered are those of mother-of-10 Jean McConville, from West Belfast, and Crossmaglen pensioner Charles Armstrong.
Three others - Joe Lynskey, Columba McVeigh, and Captain Robert Nairac - have yet to be found. Those who provide information to the organisation can do so in confidence and it can only be used to trace burial sites.
Former Cistercian monk Mr Lynskey was kidnapped in west Belfast in August 1972, while British soldier Mr Nairac was taken in South Armagh and killed by the IRA in 1977.
Mr McVeigh, from Donaghmore, Co Tyrone, was abducted, shot and secretly buried by the IRA in November 1975.
Sir Kenneth, who was previously head of the Northern Ireland civil service, said: “It has been an honour and a privilege to serve as Commissioner of the ICLVR but after 20 years it is time, reluctantly, to hand over the reins.
"I am proud of the work that has been done by the Commission and everyone involved, and I wish them every success for the future.”
Secretary of State Julian Smith has confirmed a recruitment process is to begin immediately to appoint Sir Kenneth's successor.
“Sir Kenneth has held the position of UK Commissioner from the very inception of the ICLVR with great passion, distinction and professionalism," Mr Smith said.
"This has been critical in the success of the work of the Commission, and its outstanding reputation not only in the UK but also internationally.
“I am grateful that Sir Kenneth will remain in post until his successor has been appointed.”