In an audio message released to the public on Thursday, Hun Sen said the latest outbreak occurred at the pagoda in the capital city Phnom Penh, with at least 45 infections confirmed so far, reports Xinhua news agency.
The pagoda had been shut down, he said, warning that any gathering at pagodas during the festival could lead to the mass transmission of Covid-19, especially the Delta variant.
"I really worry that after this festival, the number of infected people and deaths will increase. That can pose serious risk to the nation and can destroy our plan to reopen schools," said Hun Sen.
"I'd like to urge the health ministry to consider whether we can suspend this festival or not," he said.
"If it cannot be suspended, the number of the festival goers must be reduced to the fewest, allowing only two or three persons to bring food and other necessities to the monks at the pagodas."
The two-week Kan Ben festival began on Wednesday throughout Cambodia.
During the period, Buddhists visit pagodas to make offerings to monks in order to dedicate to their relatives and loved ones who had passed away.
Devotees believe that everything they offer to the monks will reach their dead ancestors or relatives and in return, the dead will bless them with luck, health and wealth.
Kan Ben is part of the Pchum Ben festival or the Ancestor's Day, which is one of the important festivals in Cambodia.
This year's Pchum Ben festival falls on October 6.
The Southeast Asian country has so far reported 106,619 confirmed Covid cases and 2,176 deaths.