The magazine says it has documents showing that Boeing, the helicopter's manufacturer, had agreed with software contractors that the FADEC was the cause of the 1989 accident and that the system needed to be redesigned.
The claims are a new twist in the controversy over the Chinook crash on the Mull peninsula which killed 29 people, including senior figures involved in Northern Ireland security.
Computer magazine Computer Weekly claims the minister unintentionally misled MPs over an earlier accident involving the same type of helicopter in 1989, saying that it was not caused by the Chinook's FADEC computer engine software.
Those campaigning on behalf of the two pilots blamed for the 1994 crash have always questioned whether the FADEC system could have caused the accident.
The new disclosures come in the latest edition of the magazine and concern an incident involving a Ministry of Defence Chinook helicopter in 1989.
The magazine says it has documents showing that Boeing, the helicopter's manufacturer, had agreed with software contractors that the FADEC was the cause of the 1989 accident and that the system needed to be redesigned.
After the incident, in which no one died, the MoD successfully sued a number of companies.
In the House of the Commons last month, Dr Moonie denied the legal action was over the performance of the FADEC.
However, according to Computer Weekly, the MoD's legal papers show that ministry's US lawyers won their case by showing that test procedures were adequate and that the accident was caused by the design of FADEC.
Inquiry call
Computer Weekly says there is no suggestion the minister deliberately misled the House of Commons, adding he was reading from a text prepared by his officials.
However, the latest disclosure is bound to be seized on by those wanting to see a new investigation into the crash on the Mull of Kintyre.
Independent MP Martin Bell last month called for the re-opening of an inquiry into the crash.
Mr Bell said the MoD had been guilty of "stonewalling" attempts to have the crash re-assessed and called for new evidence to be taken into account.
The official verdict found pilot error was to blame, but the families of the two pilots, Flt Lts Jonathan Tapper and Rick Cook, have consistently disputed the findings.