The summons came after the UN Observer Mission in Georgia on May 26 issued a report concluding that a Russian jet was responsible for shooting down the Georgian drone. The report contradicts claims by Abkhazia's separatist leadership that the drone was downed by Abkhaz forces.
Georgian President Mikheil Saakashvili hailed the report, which he said "directly blames the Russian Federation for aggression against Georgia."
But Kovalenko, speaking after his meeting with the Georgian foreign minister, firmly rejected the UN mission's claims. "Let me repeat it once again: the data used by the UN mission representatives raises serious doubts," he said. "I'm talking chiefly about the video, which has now already spread across the world, and the radar data."
The UN report says a video taken by the drone before being destroyed shows a fighter jet firing a missile in its direction. The UN mission, which has been in Georgia since Abkhazia and South Ossetia broke away from the central Georgian government in the early 1990s, concluded that the jet was either a Russian-made MiG-29 or Su-27 -- neither of which Abkhazia owns.
The report, based on radar records, says the fighter jet then flew back into Russian airspace.
The European Union was quick to throw its weight behind the United Nations and urge Moscow to explain its actions.
"This report is critical, or should I say rather critical of the Russian Federation, but it is not without criticism of Georgia, either. I mean, it's a balanced report and we think that those who have been found responsible should explain themselves," said Slovenian Foreign Minister Dimitrij Rupel on behalf of the European Union at the end of a meeting of foreign ministers in Brussels on May 26.
While the UN report branded Moscow's actions as "fundamentally inconsistent" with the 1994 cease-fire between Georgian and Abkhaz forces, it also said Georgian overflights of Abkhazia were in breach of the agreement.
Russia, which has some 2,500 peacekeeping forces in Abkhazia, has yet to recognize the sovereignty of either Abkhazia or South Ossetia. But it maintains close relations with both regions and provides them with financial support and Russian passports.
Former Russian President Vladimir Putin last month angered Tbilisi by ordering the government to upgrade ties with the two separatist regions.
RFE/RL's Georgian Service contributed to this report