Afghan President Hamid Karzai has criticised the first joint operation by Russian and US agents to destroy drug laboratories in his country.
Mr Karzai said he had not been informed of Russia's participation - a sensitive issue in Afghanistan ever since the Soviet occupation ended 21 years ago.
He called it a violation of Afghan sovereignty and international law.
Russia said more than a tonne of heroin and opium, with a street value of $250m (£157m), was destroyed in the raid.
Officials in Moscow have in the past accused coalition forces in Afghanistan of doing little to tackle drugs, and thereby helping to sustain the estimated 2.5 million heroin addicts in Russia.
On Friday, the head of Russia's drug control agency said its agents had taken part in an operation on Thursday to destroy a "major hub" of drug production about 5km (three miles) from the Pakistani border, near the city of Jalalabad.
Viktor Ivanov said that along with 932kg (2,055lb) of high-grade heroin and 156kg (345lb) of opium, a large amount of technical equipment was destroyed.
But in a strongly worded statement on Saturday, President Karzai's office alleged that Russian military personnel had taken part in the "illegal" raid.
"While Afghanistan remains committed to its joint efforts with the international community against narcotics, it also makes it clear that no organisation or institution shall have the right to carry out such a military operation without prior authorisation and consent of the government of Afghanistan," it said.
"Such unilateral operations are a clear violation of Afghan sovereignty as well as international law, and any repetition will be met by the required reaction from our side," the statement added.
Mr Karzai said Afghanistan wanted friendly ties with Moscow, but that the relationship had to be based on mutual consent.
A senior source in the delegation of Russian President Dmitry Medvedev, who is currently on a visit to Vietnam, told the AFP news agency on Sunday that Kabul's reaction to the anti-drug operation was "simply surprising and incomprehensible" because "the Afghan interior ministry participated in this operation".
The BBC's Quentin Sommerville in Kabul says Afghanistan's elite counter narcotics force did participate in the operation but it appears that the president's office was not informed of who would accompany them.
Afghanistan's interior ministry said it thought that only Russian observers rather than Russian troops were to take part, our correspondent adds.
The president's national security adviser, Rangin Dadfar Spanta, said Nato officials had apologised in private but that he wanted a public declaration.
Earlier, the Nato-led International Security Assistance Force (Isaf) said it had killed at least 19 Taliban fighters who tried to storm a combat outpost in the eastern province of Paktika under cover of darkness.
The militants attacked from all directions, using rifles, rocket-propelled grenades and mortars, it added. Troops at the camp had to call in air support to repel the assault.
Five coalition soldiers were wounded in the fighting.