Salokhiddin Azizov, a 20-year-old migrant worker from Tajikistan was murdered and decapitated in a forest near Moscow on December 6. Azizov's head was later found in a rubbish dumpster.
A group calling themselves the Combat Organization of Russian Nationalists has allegedly claimed responsibility for the attack.
"Such incidents often take place against the background of xenophobia, race hatred and nationalism," Davlat Nazriyev, a spokesman for the Tajik ministry, said citing the protest note.
The ministry urged Russia to take all possible measures to prevent further crimes against Tajik nationals temporarily living in Russia.
Investigators said earlier that the two Tajiks, aged 20 and 22, were returning from work through a local wood last Friday night when they were attacked by unknown assailants.
One of the men, who was hit in the head, somehow managed to escape his attackers, who were described by eyewitnesses as being of "Slavic appearance."
The decapitated body was later discovered by the brother of the murdered man, who was informed about the attack by the surviving victim.
According to the Russian non-governmental organization SOVA, 68 people died and 262 were injured in racially motivated attacks in the country in the first eight months of this year. Eighty-five people died in race-hate murders in 2007 in Russia.
