"These are baseless charges," Khaled al-Jarrallah, undersecretary of the Foreign Ministry, said on Saturday. He added they were a cause of "astonishment and discontent" in this small oil-rich country in the Gulf.
On Thursday, Russia's federal security service chief, Nikolai Patrushev, said his agency had uncovered spy activity that was being conducted under the cover of non-governmental organisations from the United States, Britain, Kuwait and Saudi Arabia.
He suggested foreign governments were using the NGOs to gather classified information in Russian regions and support changes of power in former Soviet republics.
Patrushev mentioned Kuwait's Social Reform Society and the Saudi Red Crescent by name, in addition to the British medical aid group Merlin and America's Peace Corps, which pulled out of Russia in 2003 amid spying allegations.
Social Reform Society
Al-Jarrallah said the Russian Foreign Ministry has been informed of Kuwait's rejection of the allegations.
He said the activity of the Social Reform Society, a Muslim fundamentalist group, was very limited and controlled in Russia and the former Soviet republics.
The group could not be immediately reached for comment.
Patrushev's remarks to lawmakers reflected concern in Moscow as President Vladimir Putin's Kremlin grapples with waning regional influence following the ascent of pro-Western governments in ex-Soviet states. Popular uprisings sparked government changes in Georgia, Ukraine and Kyrgyzstan over the past three months.
The Kremlin is also worried about outside influence within Russia amid US accusations of backsliding on democracy.
On Friday, a statement from the US Embassy in Moscow sharply rejected Patrushev's NGOs espionage charges.