"Migrants live in modular housing units and receive all the necessary services, and they will be living there until September," Rimantas Petrauskas, deputy commander of the State Border Guard Service, told the public broadcaster LRT.
"The units are rented to us and we pay a monthly fee for both the units and the services provided," he said. "In order to save both European and Lithuanian budget funds, we will hand over the units to the contractor."
After the closure of the Medininkai facility, four such registration centers will continue to operate in Lithuania: in Pabrade, Rukla, Vilnius and Kybartai.
The five centers currently house around 1,400 irregular migrants in total.
Almost 4,200 irregular migrants crossed into Lithuania from Belarus illegally last year.
Lithuania calls the unprecedented influx of migrants from Belarus, which began about a year ago, a "hybrid attack" by the Minsk regime.