Anatoly Kuznetsov, head of the Federal Migration Service, said the immigrants entered Russia legally but remained past the 90-day deadline for departure, RIA-Novosti reported.
"There are now over 3 million people who have stayed in the Russian Federation longer than they were legally permitted to," Kuznetsov said.
Kuznetsov said immigration is accelerating, with 14 percent more foreign-born people in the country this year than at the same time last year. The estimated number of immigrants in Russia legally and illegally is 5 million.
Other estimates of illegal immigration are higher.
Muhammad Amin Majumder, president of the Federation of Migrants, in a letter to President Vladimir Putin seeking amnesty for illegal immigrants put the number of 10 million, Izvestia reported.
The Organization for Economic Cooperation and Development reported in 2012 that Russia has more illegal immigrants than any other country, making up about 7 percent of its workforce.