The head of the regional health service earlier said 19 people had been killed but Russia's Investigative Committee reported a lower number in a later statement.
The accident occurred during the night near the town of Pokrov, some 110 kilometres (70 miles) east of the Russian capital.
"According to preliminary information, 16 people, including a child, have been killed," the Investigative Committee said.
"Other passengers, including minors, have been taken to hospital with various injuries. The number of dead and injured is being ascertained."
The committee said it had opened an inquiry.
The regional interior ministry said the bus broke down on the level crossing.
"There are no victims among the train passengers," the ministry said, releasing pictures of the wreck of the bus near the railway track.
The foreign ministry of neighbouring Kazakhstan said that the two bus drivers, one of whom was killed, were Kazakh nationals.
It also said that 55 nationals of Uzbekistan were on the bus, the Interfax news agency reported.
Road accidents are common in Russia. Seventeen people were killed in August when a bus carrying construction workers veered off a pier and plunged into the Black Sea.
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