Tim Sloth Joergensen had come under fire after it was disclosed that defense IT chief Jesper Britze was behind an Arabic translation of the controversial book "Ranger _ At War With The Elite" that was sent to Danish media.
The book was written by former special forces soldier Thomas Rathsack and describes a Danish elite army's missions in Iraq and Afghanistan. The armed forces tried unsuccessfully to stop it from being published, saying it would be a threat to forces operating abroad.
Among other things, Defense Minister Soeren Gade said the Arabic translation could give Taliban tips about how to target Danish soldiers in Afghanistan.
In one case in the book, Rathsack recalled an undercover operation during which members of the unit, disguised in Afghan clothing, escorted a secret agent code-named "Eric" from an unidentified coalition force.
Britze was suspended after the revelations.
"The recent events have obviously weakened the surrounding world's trust for the defense," Sloth Joergensen said in a statement on Sunday that announced his resignation.