Specialists from the Independent Commission for the Location of Victims’ Remains (ICVLR) had spent several weeks digging on land at Oristown, Co Meath but failed to find remains of Joe Lynskey.
He was kidnapped in west Belfast in August 1972 and became known as one of the Disappeared.
Jon Hill, senior investigator with the ICLVR said: “It’s always deeply disappointing when a search is unsuccessful.
“The information we were working from was given in good faith and warranted further investigation.
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“Unfortunately that has not produced the result that we all hoped for.”
During a previous search at nearby Coghalstown in 2015 the remains of Kevin McKee and Seamus Wright were recovered.
Mr Hill said more information was needed to find Mr Lynskey.
Meanwhile, his niece Maria Lynskey, who visited the site on the first day of the search and has closely followed the process, said she retained hope.
“All I can do is to hope and to pray,” she said.
“Hope that there is someone out there who knows something and pray that they will have it in their heart to help us to bring Joe home for the Christian burial that he has been denied for nearly 50 years”.
Some 16 people were abducted, killed and secretly buried by republicans in the 1970s and 1980s. They included mother-of-10 Jean McConville, father-of-five Charlie Armstrong and 21-year-old Peter Wilson who had learning difficulties.
Collectively they became known as the Disappeared victims of the Troubles.
In addition to Joe Lynskey, the remains of Columba McVeigh and Robert Nairac have yet to be recovered.
The ICVLR was set up following the 1998 Good Friday Agreement to help recover the remains.
Anyone with information on the Disappeared should contact the ICLVR on 00800 555 85500, by writing to ICLVR, PO Box 10827, Dublin 2. or via the website www.iclvr.ie.