The sites are three of 56 across the UK that will be sold as part of a long-term strategy to reduce costs and improve efficiency.
The sites are in County Down - Abercorn Barracks, Ballykinler; Kinnegar Logistics Base, Holywood; and Volunteer Gliding School at Newtownards Airfield.
The move was announced by Sir Michael Fallon, the defence secretary.
Sir Michael said it would deliver better value for money and release enough land to build 55,000 homes.
It is estimated that about Â£140m will be saved over the next decade by selling off the sites, which Sir Michael said would be reinvested in creating "areas of military expertise" in locations across the country.
However, Strangford MP Jim Shannon described the moves as "backwards" and "illogical".
The MoD previously said it is considering knocking down the 200 houses at Abercorn Barracks.
"It would be a rather backwards step because I think they should be retaining the accommodation for use as social housing," he said.
He added that it appeared that the Kinnegar base would move to Palace Barracks nearby and it was "unconfirmed" as to whether any jobs would be lost because of the move.
He said the decision to sell two hangars at Newtownards Airfield was an "unbelievable step".
"There is no potential for housing to be built at this site. The decision hasn't been thought out clearly, particularly as we recently got funding for the air cadets."
Three defence sites in Northern Ireland will be sold by 2040 as part of a Ministry of Defence (MoD) land review.