Tajikistan's foreign ministry summoned Russia's ambassador on Monday to protest over what it described as unfair treatment of its citizens by Moscow, in a rare dispute between post-Soviet allies, Reuters reports.
It said it was seriously concerned with frequent cases where Tajik citizens were treated in a deliberately negative way.
The ministry made no mention of Russia's arrest of several men that Moscow said were from Tajikistan following a deadly attack on a concert hall on the edge of the capital on March 22.
The Tajik ministry said in a separate statement on Sunday almost 1,000 of its citizens trying to enter Russia had been stranded in Moscow's Vnukovo airport since April 27 "without appropriate sanitary conditions being provided to them".
It said 27 Tajiks have been deported and 306 more have been put on a list of people to be deported from Russia.
"Such restrictive measures are only being taken with regards to citizens of Tajikistan," it said. Tens of Tajiks were also stuck in other Moscow airports, it added.
Russia Foreign Ministry spokeswoman Maria Zakharova said on Monday that Russia has temporarily tightened controls on its border as a measure to prevent terrorism, but was taking steps to resolve long delays on the frontier.
"We especially stress that such steps are of temporary nature and do not take into account the nationality of those arriving (in Russia)," she said.
Tajikistan is a member of a Russian-led security and trade blocs and hosts a Russian military base. Its economy depends heavily on remittances from more than a million Tajik migrant labourers working in Russia.