Milashina said on her Facebook site unknown assailants "viciously beat" her and her friend as they were returning home after work.
Milashina said she suffered injuries to her face and head and that police who later arrived "were no help."
Officials of "Novaya gazeta" said that so far they have no reasons to link the attack with Milashina's professional activities. The newspaper, however, has accused the police of being slow to respond to the attack.
Milashina has been honored by Human Rights Watch for her work in covering human rights violations in Russia.
She was friends with slain Russian journalist Anna Politkovskaya, who also worked at "Novaya gazeta," and was one of the last people to see rights activist Natalya Estemirova in Chechnya.
Estemirova was killed in July 2009, one day after Milashina left Chechnya.
Milashina was also attacked in Beslan in the aftermath of the hostage crisis at a school there in 2004.