"The two suspects arrested during the inquiry into the murder of Salim Khan Yandarbiyev have appeared before the prosecutor, who, after questioning, brought charges of murder against them," said a Qatari spokesman.
The spokesman gave no details about the suspects, but in a vehement protest from acting foreign minister Igor Ivanov, Moscow revealed the men were Russian security agents.
A third Russian agent was also arrested but subsequently freed.
"The authorities' attempt to charge them with Yandarbiyev's murder is baseless, they are not in any way involved in this incident," Ivanov said, adding that "such insinuations can only be interpreted as provocation".
The trio had been arrested in Doha last week, Ivanov said, adding that "the arresters used weapons and brute force".
"Qatar's authorities not only seized Russian citizens by force, but also did not immediately inform the embassy of it, violating the most elementary norms of international law," Ivanov fumed.
"I am trying to settle this through diplomatic channels"
According to the Russian foreign ministry's statement published overnight, all three "were in Qatar legally and worked on information and analysis within the framework of the international campaign against terrorism".
Russia's foreign intelligence service said earlier this month that it had nothing to do with the death of Yandarbiyev, who was killed when his car blew up on 13 February, the first such incident in the Gulf state.
Flurry of activity
Despite the denials, the murder has coincided with a flurry of diplomatic activity between Doha and Moscow.
"I have no exact information about the two Russians" facing the charges, ambassador Viktor Kudriavdsev said, adding: "I am trying to settle this through diplomatic channels."
A senior Russian foreign ministry official, Mikhael Bogdanov, visited Doha on 20 and 21 February and discussed bilateral relations with Foreign Minister Shaikh Hamad bin Jassim bin Jabr al-Thani.
Official sources said the visit followed a phone call from Ivanov to his Qatari counterpart.
Yandarbiyev, whose name figured on a UN blacklist of people suspected of links to the al-Qaida network and the ousted Afghan Taliban government, briefly headed Russia's war-torn separatist republic of Chechnya in the mid-1990s.
The 51-year-old, who lived in Qatar "temporarily" for nearly three years with his family despite a Russian extradition request, died and his 13-year-old son was wounded when a blast targeted their car as they returned from Friday prayers at a Doha mosque.