Military spokesman Ruwan Wanigasuriya said the 512 Brigade has already released 18 of the 45 houses.
"The rest of the houses will be handed back to the civilians within the next few months while the construction of new buildings and infrastructure for the brigade have already started", Wanigasuriya said.
Since the end of the war against the LTTE in 2009, Sri Lankan Army came under international pressure to reduce its military strength in former conflict zones in order to restore normalcy.
The number of troops now stationed in Jaffna stood at 15,000, down from 50,000 during conflict times, the military said.