The Official Secrets Act should be suspended to allow former intelligence officers to give evidence about alleged cover ups during the child abuse inquiry, Amnesty International said.
An ex-soldier involved in military intelligence has claimed he was told to stop investigating sexual abuse at a boys' home in the 1970s.
Brian Gemmell told the BBC he was ordered to halt his probe into Kincora Boys' Home in Northern Ireland by a senior MI5 officer in 1975 after presenting a report on the allegations.
Patrick Corrigan, Amnesty International's Northern Ireland director, said: "The focus must be the protection of children, rather than officials and their dirty secrets."
Home Secretary Theresa May has faced widespread calls from politicians and lobbyists in Northern Ireland to include Kincora in the child abuse inquiry which was established following revelations about serial sex offenders like Jimmy Savile.
The inquiry was set up to examine how public bodies handled their duty of care to protect children from paedophiles.
Mr Corrigan added: "The Home Secretary must announce the inclusion of Kincora in the inquiry and an exemption so that army officers and others bound by the Official Secrets Act can finally speak freely."
In 1981 three senior care staff at the east Belfast Kincora home were jailed for abusing 11 boys and i t has been claimed that people of the "highest profile" were connected.
Mr Gemmell said he found out about the abuse through two sources, including an agent called Royal Flush, while he was gathering information about loyalists.
"I was summoned to go and see him (the MI5 officer). I went up thinking he was going to be pleased with me," he said.
"He bawled me out. He was rude and offensive and hostile.
"He told me not just to stop any investigation into Kincora, but to drop Royal Flush."
It comes during a public inquiry in Northern Ireland into institutional child abuse between 1922 and 1995, which faced possible suspension last month due to a lack of money as coalition parties were at loggerheads over the latest budget.
Retired judge Sir Anthony Hart, who is leading the Historical Institutional Abuse Inquiry (HIA), has said the inquiry "does not have sufficient powers" in its present form to investigate issues relating to the Army or MI5. Sir Anthony also said that "there may be benefits to the UK-wide inquiry examining the relevant allegations into Kincora Boys' Home".
Northern Ireland's First Minister Peter Robinson said: "I want to see a full investigation into the terrible abuses which occurred in Kincora. Having received this communication from Sir Anthony, it is clear that the proper route to fully investigate the abuse at Kincora Boys' Home is to have it included in our United Kingdom's Child Abuse Inquiry.
"I will be writing to the Prime Minister and alerting him to Sir Anthony's concerns. I will be urging the Prime Minister to ensure that Kincora is included in the terms of reference governing the inquiry established by Her Majesty's Government."
Earlier this month, another former Army officer, Colin Wallace, said any new investigation of Kincora must have access to information from intelligence agencies.