The plans were revealed by The Guardian, which has seen a letter signed by permanent secretary of the MoD Ursula Brennan, which is being sent to all staff explaining why the cuts are necessary.
The latest jobs cull is on top of defence secretary Liam Fox's plans announced last week to cut 7,000 military jobs between 2015 and 2020.
A spokesperson for the MoD said: "It's a broad brush figure [at this stage]. There aren't any areas particularly being targeted or not targeted."
However, the trade union Public and Commercial Services (PCS) said that while there are no targeted IT redundancies in the MoD at the moment, there has been general trawl for people across the department to volunteer for redundancy.
A spokesperson for the union said that 5,500 people are understood to have done deals under the trawl.