The clash took place between followers of Uday Singh and activists of the breakaway group of the sect, police said.
When the religious congregation, organised by the Thakur Uday Singh group, was on, followers of the breakaway faction stormed the venue.
They demanded a meeting with Thakur Uday Singh and another religious leader Mata Chand Kaur, police said.
When their demand was turned down, two shots were fired in the air in the presence of Thakur Uday Singh, they said.
Uday Singh escaped unhurt and left the venue under heavy police escort.
A police official said two shots were fired and two persons from both the groups received minor bruises in the clash.
Police rounded up people from both the groups and registered a criminal case against two persons belonging to the breakaway faction.
Thakur Uday Singh was announced legal and spiritual successor of Namdhari sect after the demise of Satguru Jagjit Singh recently.
The breakaway group is led by Thakur Dilip Singh who was keen to become the sect head but did not succeed.
Police said Dilip Singh was not present when the clash erupted at the congregation.