Russia's Investigative Committee said in a statement that Rinat Akhmetchin had failed in his duties to contain the spill, which environmentalists say is the largest to have ever hit the Arctic.
The spill of over 21,000 tonnes of fuel took place after a reservoir collapsed on May 29 at a power plant operated by a subsidiary of metals giant Norilsk Nickel in the city.
Much of the fuel leaked into local rivers and lakes, creating red stains so big that they could be seen from space. Clean-up efforts are expected to take years and cost Norilsk Nickel nearly $150 million.
The committee, Russia's top federal investigation agency, said that after learning of the spill Akhmetchin "did not take proper measures to respond to the emergency situation and deal with its consequences."
It said he failed to organise a proper environmental response and monitoring of the spill, or to coordinate local efforts.
Akhmetchin, a 55-year-old who has headed the city government since September 2017, faces up to six months in prison if convicted.
Several staff at the plant have also been detained over the spill, which Greenpeace Russia has said is comparable to the Exxon Valdez disaster off the coast of Alaska in 1989.
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