Hundreds of thousands of fish have been washed up on the shores of Lake Cajititlan in the Mexican state of Jalisco over the past week.
Almost 50 tonnes of dead popoche chub freshwater fish have been removed from the lake.
The local authorities said it was part of a "natural cycle" but state officials said it was due to the lake's "poor management".
More fish are expected to wash up over the next days.
Jalisco's secretary for the environment, Maria Magdalena Ruiz Mejia, denied "categorically that this is a natural and cyclical phenomenon".
"We have no evidence to support that it is natural and cyclical, to the contrary, we have a series of variables which lead us to believe this phenomenon is not only recurrent and becoming more frequent and severe, but also that it is caused by the poor management of the body of water," she said.
Ms Ruiz Mejia said mud from local wastewater treatment plants could be to blame for the mortality.
When questioned by local journalists whether her office had evidence to support her allegation she said state authorities had been denied access to the plants and could therefore not yet carry out an investigation of the premises.
The state authorities have issued an environmental alert for the lagoon, but said human health was not endangered.
The lake is 9km (5.6 miles) long and 2km wide and is located north of the much bigger Lake Chapala, about 500km west of Mexico City.