Devyani International, which operates the US fast-food outlets in Nepal, said the restaurants closed in Kathmandu on May 13 after a scuffle allegedly broke out between workers and managers.
"We have closed down indefinitely," said Rohit Kohli, the company's Kathmandu-based director.
Kohli said a local union had demanded their members stop working at 6pm to give them time in the evenings to repair damaged homes and help family members since the massive quakes.
More than 8,700 people died in the two quakes that hit Nepal on April 25 and May 12, destroying nearly half a million houses.
Kohli accused union members of attacking his staff who continued to work later in the evening as directed by the restaurants.
"We cannot operate in an environment like this," Kohli told AFP.
"We have been suffering from labour problems for five years and it has crossed our tolerance levels."
Local union leader Sita Ram BK told AFP: "Many of us have lost our homes and even family members."
"We can't be forced to work like nothing has happened," he said.
"We are hearing rumours of closure, but they have not told us anything. We want them to open the restaurants and let us work."
Read:Going the extra mile: After earthquake, two men backpack to Nepal
KFC and Pizza Hut, Nepal's only international fast-food chains, opened their first branches in the Himalayan nation in 2010, generating long queues of locals wanting to sample their offerings.
Their arrival was seen as a sign of an improving environment for foreign firms in a country ravaged by a civil war between 1996 and 2006, when Maoist rebels agreed to a peace deal with the government.
In 2012, the restaurants closed down temporarily for 35 days, saying staff had attacked and threatened to kill branch managers over a labour dispute.
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