"Double standards are inadmissible," he said after a meeting with his NATO counterparts, dominated by efforts to boost cooperation in the fight against international terrorism.
"Everyone agreed that we must do away" with such double standards, he told reporters.
The perpetrators of the September school massacre in Beslan, southern Russia, "cannot be considered as partisans or insurgents, but simply terrorists," along with those who train and fund them, he said.
Lobby groups like Amnesty International have accused Moscow of sacrificing protection of human rights in its anti-terrorism clampdown centred on the breakaway republic of Chechnya.
But Ivanov said that no Russian soldier under his responsibility had been found guilty of violating anyone's rights in the last year.
"Respect for human rights is improving slowly but surely" in the Russian federation, he said, noting a recent visit to Moscow by European human rights envoy Gil Robles.
But he said: "War is war. We are fully morally entitled to take any action within our power to exterminate terrorists."