Fifty-eight people were moved out of a similar hangar at the Kabeliai border station on Monday.
"No people from socially vulnerable groups, such as pregnant women, minors or families with children, had been accommodated in the hangars," Mindaugas Bajarunas, the ministry's spokesman, told BNS.
People housed in the heated hangars have been transferred to modular housing units, according to the spokesman.
"Most of these migrants have been accommodated in the foreigners registration center in Pabrade," he said.
The ministry said in late September that all migrants had been moved out of tens. In October, it said all migrants had been moved out of temporary accommodation provided by municipalities.
Almost 4,200 migrants, mostly Iraqi citizens, have crossed into Lithuania from Belarus illegally so far this year.
Vilnius accuses the Minsk regime of orchestrating the unprecedented migration influx, calling it "hybrid aggression"