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Dilma Pena has asked to resign from her post, local paper Folha de S. Paulo reported, citing comments made by São Paulo governor Geraldo Alckmin.
During a webcast of a special state parliamentary committee meeting, Pena seemed visibly disturbed by the plight of the region.
She said, citing Brazil's waterworks technology foundation FCTH, that thousands of years could pass before the country experiences the same combination of weather events that led to the current drought.
"According to the country's waterworks technology foundation FCTH, this type of weather condition will not occur for another 3,338 years." Pena said.
Alckmin has reportedly asked the executive to remain in post until at least December.
On Tuesday, the state's largest water supply system, Cantareira, was operating at a record low, 3.3% of capacity. To help tackle the shortage, Sabesp is extracting 106Bl of Cantareira's deeply settled water, known as "dead volume" water.