The average payout for senior fixed-term appointees was 31,890 but the highest was 84,563, according to figures released by Defence Secretary Bob Ainsworth.
For permanent MoD staff at senior civil service level, the average bonus for 2008-9 was 8,177 with a maximum payout of 15,000.
Senior fixed-term appointees are either consultants brought in from outside the civil service or seconded from other departments, said the Cabinet Office.
Taxpayers' Alliance spokesman Mark Wallace labelled the payments "obscene" when soldiers were risking their lives in Afghanistan for a "pittance".
He said: "I would say it is obscene such massively large amounts are being handed out to the office desk warriors in the MoD while our soldiers in Afghanistan are forced to fight with inadequate kit and in return for a pittance.
"Bonuses have their place but given the MoD's financial problems and the gross inequality between civil servants and soldiers these are totally inappropriate."