KUALA LUMPUR, Sept 4 (Reuters) - Malaysia began culling about 50,000 pigs in southern Malacca state on Tuesday following complaints about the stench and pollution the animals had caused, officials said, but denied there had been a disease outbreak.

Ethnic Chinese in multiracial Malaysia relish pork, but the country's majority Muslim population frowns on consumption of the meat.

"The operation has started and within 12 hours they have to slaughter close to 50,000 pigs," said a veterinary department official in the administrative capital of Putrajaya.

"I think many farms were operating without proper licences and local people were complaining about the smell and water pollution."

Malacca does not want to emerge as Malaysia's biggest pig producer, with a swine population estimated at 160,000, state chief minister Mohamad Ali Rustam said last month, according to media reports.

Farmers said the pigs were perfectly healthy and did not cause any pollution.

"We don't know if they are going to shoot the pigs or just bury them alive," said an official of the Federation of Livestock Farmers' Associations of Malaysia.

"It is not fair, these pigs are healthy and they are not really a source of pollution because many farms do practice good waste disposal habits," said the official, who declined to be named.

In China, poor returns on pig raising and an unusually virulent outbreak of Porcine Reproductive and Respiratory Syndrome (PRRS), also known as blue ear disease, have reduced the nation's pig population and pushed up the cost of meat.