One of the protesters told the Associated Press that he was in the mosque when troops entered and opened fire, although no-one was injured.
At least two bullets hit the door of the mosque, said Kazim Allayar, deputy provincial governor, during a visit to the site of the alleged incident.
Government officials will meet with Polish forces on Saturday to find out if they were involved, he said.
Lieutenant Commander Chris Hall said, a Nato spokesman, said they were no reports of international troops being in the area where Thursday's incident allegedly occurred.
Robert Rochowicz, a spokesman for Poland's defence ministry, said he had "no information at all about any kind of incident concerning Polish troops in Afghanistan".
International forces have been battling fighters loyal to the Taliban, which has been resurgent in Afghanistan's southern provinces in recent months.
Nato and the US have both been criticised by the Afghan government over a series of raids in which civilians were killed.
Hamid Karzai, the Afghan president, has urged international forces to do more to respect the local population and prevent civilian deaths.