Russia’s Interfax news agency reported on Saturday the two Qataris were accused of having links to armed groups in the Russian territories – making reference to the breakaway province of Chechnya.
The arrest came a day after Russian officials angrily denounced Qatar’s arrest of two of its intelligence agents in Doha and demanded their release.
The officials had warned of a diplomatic row between the two nations over the affair.
Qatar's interior ministry had announced on Thursday two men had been charged with assassinating former Chechen president Salim Khan Yandarbiyev through a car bomb attack.
Russia has flatly denied the accusations against the detained men and insisted it was not involved in the Chechen leader's assassination.