They include a powerful car bomb blast that killed three policemen in the eastern Georgian city of Gori in February.
The blast went off on February 1 outside the regional police headquarters in Gori, 80 kms (55 miles) west of the capital, Tbilisi.
Mr Merabishvili said an investigation has “revealed that Russian colonel Anatoly Sysoyev organised a group of saboteurs who were trained on Russian territory.”
“The group was responsible for several terrorist attacks and organised the attack in Gori,” he said.
Sysoyev is alleged to be part of the Russian army’s intelligence directorate and was frequently in touch with officials in Moscow.
The allegation was made during a filmed confession by Giya Valiyev, one of the men charged with carrying out the Gori attack.
It’s further alleged the Russian colonel travelled to the separatist region of South Ossetia, inviting Valiyev to join military intelligence.
After the bomb attack, Valiyev said he received $US1,000 ($A1,310) from Sysoyev, who then returned to Russia.
Russia immediately denied the allegations.
“No Russian state institution could have had any relation to this,” said Yevgeny Ivanov, spokesman for Russia’s embassy in Tbilisi.
A statement from the Russian foreign ministry warned the allegations would not help develop bilateral relations.
“The people… (who were named) are not listed or employed in any official Russian structure,” the statement added.
Georgian President Mikhail Saakashvili sought to play down the diplomatic crisis later Monday.
“We do not want to use this information for confrontation. We wish to cooperate with Russia, its agencies and government in full in the cause of fighting terrorism, as these people not only struck a blow against Georgia, they are a problem for Russia as well,” Saakashvili said.
The findings of the investigation into the Gori attack fuelled tensions between Moscow and Tbilisi.
Tensions have been high between Moscow and Tbilisi since Georgia’s pro-Western President came to power in early 2004.
He vowed to bring the separatist territories of Abkhazia and South Ossetia, which are supported by Moscow, under Georgia’s sway.