Iran says it is arming the Afghan Northern Alliance
Russian Defence Minister Sergei Ivanov said the deal "is not a secret one, it complies with all norms and standards of international law and is almost identical in content to similar documents that Russia has signed with many countries".
His Iranian counterpart, Ali Shamkhani - who is on a four-day visit to Russia - warned at the start of his trip that Iran would confront any US aircraft that tried to use Iranian airspace for an attack on Afghanistan.
The two ministers discussed the struggle against terrorism, particularly in relation to Afghanistan, where both Tehran and Moscow support the anti-Taleban opposition.
Mr Shamkhani's visit, originally scheduled for last month, was postponed because it would have coincided with a trip to Moscow by Israeli Prime Minister Ariel Sharon.
Co-operation
On Monday, Mr Shamkhani also confirmed officially that Iran was arming and supporting the anti-Taleban Afghan Northern Alliance and intended to continue doing so.
Earlier, the Russian Itar-Tass news agency quoted Mr Ivanov as saying Moscow was ready to use its good relations with Tehran to discuss the extent of Iran's support for the anti-terrorist operation in Afghanistan.
Since early on in the current crisis, Iran has made it clear it will not co-operate with an American-led attack on its eastern neighbour.
It has also said it will defend its own borders against encroachment from any quarter.
Defending airspace
Now the defence minister has spelled out that that would mean confronting American aircraft if they should try to use Iranian airspace for an attack.
Asked what Iran would do in such an event, Mr Shamkhani said: "We are military men, and we don't fool about. Mistakes cannot be repeated. If they are, it means it's deliberate, and we will confront them. We will defend our airspace."
That was taken to mean that Iran would tolerate an occasional accidental straying, as happened during the 1991 Gulf War, but nothing more than that, says the BBC's Tehran correspondent.
In practice, such a confrontation seems unlikely, as the Americans would not need to use Iranian airspace, even if Iran shares more than 900 km of border with Afghanistan, our correspondent says.
Mr Shamkhani's trip is the first to Moscow by an Iranian defence minister since Iran's 1979 Islamic revolution and the latest in a series of exchanges aimed at warming relations.