According to the newspaper, the children who were abused were allegedly taken from the Kincora children's home in order to be offered to men.
"There are longstanding claims that MI5 blocked one or more police investigations into Kincora in the 1970s in order to protect its own intelligence-gathering operation," The Guardian reported, quoting Amnesty International.
The UK Home Office declined to say whether any intelligence agent had been questioned regarding the situation.
Last December, British media reported that child abuse victims in the country did not trust the Home Secretary Theresa May's investigation into claims of decades-long child abuse cover-ups.
An inquiry panel was established last summer in the UK to conduct a wide-ranging investigation over allegations of child abuse dating back to the 1970s and 1980s.