Martin claimed that murders had to be approved by the political and military leadership of the IRA which meant Mr Adams.
Donaldson's murder was claimed by the Real IRA, but the informer said the Provisional IRA's South Armagh Brigade demanded Donaldson be killed in revenge for working as a British agent while operating as a senior Sinn Fein official in the Stormont parliament.
When Denis Donaldson, 55, was shot dead in County Donegal in April 2006, it had emerged that he had been a British spy within both the IRA and Sinn Fein.
"I was shocked and surprised when I heard about Denis Donaldson's murder", he said.
Gerry Adams himself has refuted any suggestion that he was in any way involved.
He added that Adams: "Categorically denies the unsubstantiated allegation that he was consulted about an alleged IRA army council decision or that he had the final say on what had been sanctioned".
In a statement, Sinn Féin MLA Gerry Kelly said the BBC Spotlight programme was "a collection of discredited conspiracy theories which relied on the claims of an anonymous paid liar and British agent".
Adams, who denies IRA membership, said Wednesday he had no role in Donaldson's slaying.
The programme claimed that it was sanctioned on foot of a request from republican Thomas "Slab" Murphy and other leading republicans in South Armargh for the objective of maintaining army discipline.
Mr Adams, who said he would have no issue speaking to police to reiterate his denial, said he was consulting with his lawyer about potential legal action against the BBC.
During the Troubles it is believed there were at least 800 informers for the British Government within the IRA and Sinn Fein.
It was revealed two months later he had been recruited by MI5 as an informant during a "vulnerable time in his life", although no more details were revealed as to when or why.