Mexicans are baffled at the sudden death of thousands of fish in a lake in the centre of the country, a dramatic intensification of a problem that no one has yet been able to explain.

Nearly 50 tonnes of dead popoche chub fish were removed at the weekend from Lake Cajititlán, a lagoon in the central state of Jalisco.

Fishermen, firefighters, town hall workers and staff from the state agricultural ministry pulled hundreds of thousands of dead popoche chub fish from the lake and buried them in a pit.

The incident comes after of a series of smaller waves of dead popoche chub in the lake in recent months, including one last week, ensuring that 2014 is already by far the worst year for the species, which has been under attack for the past few years.

The authorities in the lakeside town of Tlajomulco de Zúñiga, about 25 minutes' drive south of the city of Guadalajara, had previously blamed the deaths on "a cyclical phenomenon caused by temperature variations and the reduction of oxygen".

This weekend, the state's environment secretary, Magdalena Ruiz Mejía, ruled out natural causes and blamed "poor management of the body of water". She pointed to municipal waste water treatment facilities and promised a full investigation.

There have been complaints that a nearby tequila distillery is storing waste in containers that drain into channels that feed into the lake.

Victor Hugo Ornelas, a reporter from the Tlajomulco-based newspaper La Verdad, said it also appeared that fertilisers washed into the lake from surrounding cornfields during the rainy season could be a significant factor. The fertilisers appear to fuel the growth of algae near the surface, where the popoche chub swim.

"It is obvious that there are many sources of pollution around the lake," Ornelas said. "Fertiliser runoff in a particularly heavy rainy season could be the straw that is breaking the camel's back."

José Luis Castillo, who takes tourists around the lake in his boat, told the newspaper El Informador how the fish first attracted attention by swimming even closer to the surface than usual. "After that they died," he said. "Lots and lots have died this year."

The fish deaths are just the latest in a succession of incidents in which large numbers of creatures have been found dead in particular places, from sea lions in California to seabirds in Peru.