Moscow backs the Uzbek government in blaming the bloodshed in the town of Andizhan earlier this month on radical Islamists.
Witnesses say more than 500 people died when troops put down a popular protest. Uzbek leader Islam Karimov denies ordering troops to fire and Uzbek authorities say 169 people died, most of them "bandits".
"Putting forward a demand for an international investigation as an ultimatum is neither appropriate nor fair," said Russia's Deputy Foreign Minister Vladimir Chizhov at a meeting of Nato countries and partner states in Sweden on Wednesday.
Nato's North Atlantic Council issued a statement condemning "the use of excessive and disproportional force by the Uzbek security forces".
"We support the United Nation's call for an independent international inquiry into these events and urge the Uzbek authorities to allow such an investigation," it read.
"Putting forward a demand for an international investigation as an ultimatum is neither appropriate nor fair"
Russia's deputy foreign minister
Nato Secretary-General Jaap De Hoop Scheffer said Nato has received no response from Karimov.
Despite major concerns about Karimov's human rights record, Washington considers him an ally in its "war against terror".
The country borders Afghanistan and hosts a US airbase, receiving in exchange financing for Uzbek security forces.
Uzbekistan, a Nato partner, was invited to the meeting in the Swedish town of Are but cancelled at the last minute.
"We are gathered here as partners and partnership means trust. If one partner says it can carry out an investigation itself, that should be respected," Chizhov told reporters.
"The countries calling for an international investigation recently competed with each other hailing Uzbekistan's role as a key player in the global anti-terrorist coalition. Now they realise who they were dealing with," he said.