The suspension could lead to Lieutenant Colonel Keith Pople's dismissal from the armed forces.
Last month a military tribunal at Aldershot ruled that Lt-Col Pople had not prejudiced good order by sleeping with Lieutenant Commander Karen Pearce while evaluating her work.
Yesterday a spokesman for the MoD said: "His commanding officer suspended him while considering what administrative action might be appropriate.
"The decision to suspend rests with the CO and may be taken when a matter appears to reflect adversely on an officer's conduct or character."
Administrative action is similar to the process in civilian life for dismissing staff whose performance falls below acceptable standards.
The MoD spokesman added: "Any appropriate administrative action will be considered by the CO and if the decision is taken to proceed it will be processed through the chain of command.
"We are not able to discuss the matter further as it is in confidence between the officer and his CO."
Lt-Col Pople, 42, admitted beginning an affair with Lt-Cdr Pearce, 34, in 1993, while sharing a Whitehall office at the MoD. Both officers were married.
The affair ended soon after Lt-Cdr Pearce was posted to the aircraft carrier HMS Illustrious in April 1995.
The Army has a strict code of conduct which officers are expected to maintain in the interest of good order and discipline. The code covers many aspects of private behaviour, and adultery within the military community would be regarded as a serious breach of the code.
Lt Col Pople was suspended from a staff officer job at the headquarters of UK land forces at Wilton, near Salisbury.
Before the scandal erupted he had commanded 4 Regiment Army Air Corps.Reuse content