Rain floods Greece's largest migrant camp
The ministry said 80 tents at Kara Tepe camp had to be replaced after the downpour on Thursday.
The facility was hastily put together after the camp of Moria, Europe's largest, was destroyed in a September 8 fire.
"It makes sense that a temporary facility built in a few days will face problems. The problems are being dealt with immediately... Most of the camp was unaffected," the migration ministry said in a statement.
The new camp's 8,500 residents have complained that the new facility has basic bedding and no electricity or running water.
The ministry on Friday said 2,500 people had already moved out of the camp since last month, and another 1,300 will be allowed to relocate elsewhere in the European Union.
Read more: Greece says no unaccompanied minors remain in island camps
Germany has offered to take 1,500 asylum seekers from Greece, including former Moria residents, while France has offered to take in 900, including 500 minors from the camp.
The government wants to build a new permanent camp on Lesbos, but the plan has been held up for months by local opposition.