The Interior Ministry said the accident happened when several cars on a cargo train derailed and hit a passenger train moving on a parallel track near Naro-Fominsk, a town 50 kilometers (30 miles) southwest of Moscow.
Officials issued contradictory claims about the cause of the accident.
Footage from the crash site broadcast by Russian television showed one side of a passenger car torn away by the collision.
Nina Suslonova, the Moscow region's health care minister, told the Rossiya 24 news channel that five people were confirmed dead at the site. Dmitry Pestov, a deputy head of the Moscow region's government, later said that another person died at a hospital, the Interfax news agency reported.
Those who were injured were all in the same car.
The Emergency Situations Ministry said 45 people were injured and 25 of them were hospitalized. It said 15 were in grave condition.
The passenger train had been traveling from Moscow to Chisinau, Moldova.
Moscow's public transport department initially said the accident was caused by a crack in the rail, but the Investigative Committee said it occurred when a cargo container came loose and hit the passenger train.
Hundreds of rescue workers, dozens of ambulance crews and several helicopters rushed to the site to help the victims.