Russian Defense Minister Anatoly Serdiukov and Moscow Machine-Building Plant Avangard Chief Executive Officer Gennadi Kozhin signed the agreement.
The anti-aircraft missiles will be supplied to Russian army anti-aircraft missile batteries.
The S-400 "Triumph" anti-aircraft system became operational in 2007 as a successor system to the Soviet-era S-300.
Avangard will be the sole supplier of missiles for the S-400 system but the value of the contract wasn't disclosed, the Russian Defense Ministry reported on its Web site,
The types of missiles to be provided weren't disclosed but previous descriptions of S-400 system have included the 9M96 and 9M96E2 and the long-range 40N6E designations.
The S-400 antiaircraft system is so advanced that Russian military prohibits its export.
The S-400 is a medium- to long-range surface-to-air missile system that can effectively engage most aerial target, including aircraft, unmanned aerial vehicles, and cruise and ballistic missiles at a range of up to 250 miles and an altitude of up to 20 miles.