Seventeen people suffered serious injuries including one child, the Russian health ministry said.
Speaking on Russian television, a ministry official said the accident occurred around 12:30 pm local time (0830 GMT) between the towns of Bekasovo and Naro-Fominsk, some 80 kilometres (50 miles) southwest of Moscow, as the passenger train was travelling from the Russian capital to Moldova's capital Chisinau.
Five people died in the immediate aftermath of the accident and another died later in hospital, officials said.
The health ministry said Tuesday evening that a total of 25 were hospitalised. The emergencies ministry said there were about 400 passengers on the train.
Four of those who died and 13 of those hospitalised had been identified as Moldovan citizens, Moldova's emergency ministry said. The impoverished ex-Soviet state is largely Russian-speaking and many of its citizens work in Russia.
Moldovan Prime Minister Iurie Leanca said he was deeply grieved by the deaths and sent a message of sympathy to the injured, the government website said.
A picture released by the emergencies ministry showed one side of the passenger train completely torn away, with passengers emerging from the wreckage.
"One of the carriages of the passenger train was crushed by the freight train wagons," news agency ITAR-TASS quoted rescue coordinator Vadim Andronov as saying.
At least 500 people were involved in rescue efforts, officials said, and seven helicopters were used to ferry the injured to hospitals.
Russian Railways said in a statement that 15 wagons of the freight train had derailed, damaging at least two carriages of the passenger train.
The cause of the accident was not immediately known. Investigators were on site and officials said a criminal probe had been launched.
"The investigation is looking at three possible causes for the accident: first, the poor condition of the freight train; second, the poor condition of the track at the location of the accident; and third, a violation by personnel on the train," Tatyana Morozova, the deputy head of the regional transport investigation department, told AFP at the scene.
The driver of the passenger train, Anton Ivanov, told Life News website that his train was travelling at 95 kilometres (60 miles) per hour when he saw the approaching freight train throw up a cloud of dust and derail.
"We slammed on the emergency brakes. After that we couldn't see anything because there was a lot of dust, visibility was zero," he said.
Several hours after the accident officials said the rescue operation was over and that the remaining passengers had been evacuated from the area. Service on the line was expected to resume late on Tuesday.
The Interfax news agency quoted a local representative of French carmaker Renault saying the freight train had been carrying parts for use in its plant in Moscow.
Accidents involving Russia's outdated infrastructure are frequent, though Russian Railways in 2010 announced it was investing $11 billion in upgrades across its network of 85,500 kilometres (53,000 miles).
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