Anatoly Slyusar said over 48 payments worth 100,000 rubles ($3,900) each had so far been made, and that payments would continue over the next two days.
In line with Russia's Civil Code, 2 million rubles ($77,800) is to be paid out for each person killed in an air crash.
The Boeing-737-500, owned by Russian flagship air carrier Aeroflot, crashed on a Siberian railroad track linking Yekaterinburg and Perm, killing all 88 people onboard. A technical failure is being seen as the most likely cause of the crash.
Two experts from Boeing are to help determine the cause of the crash, the U.S. company's representative in Moscow said on Monday.
Russia's prosecutor general said earlier in the day that he was taking personal charge of the investigation.
