During a parliamentary debate on the 1994 Chinook crash on the Mull of Kintyre last week, Hoon said there had been "so much nonsense written about the subject in Computer Weekly".
Following the crash in which 29 people died, two RAF air marshals found there was no doubt whatsoever that the two pilots were grossly negligent in causing the crash.
Since 1997, Computer Weekly has campaigned for the verdict to be overturned and has published evidence that questions the reliability of the aircraft's computerised Fadec engine control system.
Hoon said, "Some of the evidence [in Computer Weekly] may be acceptable, but the way in which that journal hysterically pursues the subject does not give me cause to accept anything it says at face value".
In 1999, then home secretary Jack Straw presented a Freedom of Information award for Computer Weekly's work on the Chinook story. The award was for uncovering "persuasive evidence that problems associated with the helicopter's software had surfaced in the weeks before the accident".
In 2001, Computer Weekly received a PPA award, the publishing equivalent of an Oscar, for its work on the Chinook crash. And the Public Accounts Committee published in full a Computer Weekly report revealing inaccuracies in statements to parliament over the crash. Its subsequent report accused the Ministry of Defence of "unwarrantable arrogance".
Today Computer Weekly publishes an open letter to the minister urging him to specify what parts of the published Chinook evidence he regards as "nonsense". Otherwise he should retract his statements and apologise, it says.
The MoD said it would respond in due course.