TV footage of Friday's match in the southern city of Vlora showed the remote-controlled device carrying a flag during the match between local Flamurtari and Skenderbeu. The game was not interrupted and ended 1-1.
Team officials could not be reached for comment and police had no immediate response.
In Belgrade Tuesday, a drone carrying Albanian nationalist banner started the clashes between players from the Serbian and Albanian national teams and fueled crowd trouble.
UEFA, the governing body of European soccer, has opened disciplinary cases against both countries.