Dozens were injured and Russian officials said the death toll could rise. All of the windows and most of the side of one green carriage had gone, a Reuters cameraman on the scene said.
Russian television footage showed dazed passengers clambering off the tilting train and climbing up a grassy bank to safety after the accident.
The train had been on its way from Moscow to Chisinau, the capital of Moldova, before the collision at around 12:30 p.m. (0830 GMT) near the town of Naro-Fominsk, 55 km (34 miles) southwest of the Russian capital.
The cause of the accident was not immediately known but a criminal investigation has been opened.
"We tried to use an emergency brake. We couldn't see anything ahead, there was lots of dust. Visibility was zero," state-run RIA news agency quoted one of the drivers of the passenger train as saying.
Meeting Russian President Vladimir Putin in Shanghai, U.N. Secretary General Ban Ki-moon expressed his condolences. Putin promised a thorough investigation and aid for the families of victims.
An official from state-owned Russian Railways told reporters at the scene that five people had been killed immediately and a sixth had later died in hospital. Russian Railways said the collision occurred after 15 freight-train carriages derailed.
Viktor Yatsenko, an official with Russia's Emergencies Ministry, had earlier told a televised teleconference with other officials that 45 people had been hurt in addition to the dead. He said 15 of the injured were seriously hurt.
Most of the injured were Moldovan citizens, Moscow regional health minister Nina Suslonova said on Rossiya-24 television.
Serious accidents on Russia's 85,000 km (52,800 miles) of rail track are relatively rare but critics say the country's creaking transportation infrastructure, including its railways, badly need investment and renovation.