The contract for up to 30 missile systems would be fulfilled except in “extraordinary circumstances”, Sergei Ivanov said, without elaborating.
He stressed that, because of their technical characteristics, the missiles could not be used by terrorist groups.
The $700m (£380m) deal, signed last year, has been condemned by the US.
Washington wants all countries to stop exporting weapons to Iran. Russia insists its short-range Tor-M1 system is purely defensive.
“As far as Russia’s position is concerned, we strictly abide by all non-proliferation regimes, and when we hear reproaches that Russia is secretly helping Iran – it is just propaganda,” the Interfax news agency quoted Mr Ivanov as saying.
He made the comments following a meeting with his German counterpart, Franz Josef Jung in St Petersburg.
Russia, along with China, is strongly against attempts to impose United Nations sanctions on Iran, which the US accuses of pursuing nuclear weapons.
