Russian Deputy Foreign Minister Grigory Karasin said the issue was settled during his talks Wednesday with Azerbaijan's foreign minister.
The talks followed an incident in March when Azerbainani customs halted a shipment of Russian insulation equipment for Iran's nuclear plant. Azerbaijan released the shipment May 1.
"We have found a mutually acceptable solution to prevent such incidents from happening in the future," Karasin told reporters after the talks.
Iran is paying Russia more than $1 billion to build the light-water reactor in Bushehr _ Iran's first atomic energy plant.
The U.S. and other Western nations that fear Iran is seeking to acquire nuclear weapons have criticized Russia in the past for building Bushehr. Washington, however, softened its position after Iran agreed to return spent nuclear fuel to Russia to ensure it does not extract plutonium from it that could be used to make atomic bombs.
The U.S. and its Western allies also agreed to drop any reference to Bushehr in the sanctions resolutions passed by the U.N. Security Council, as a result of Russian pressure.
Russia says the plant's contract is in line with all international agreements aimed at preventing nuclear weapons proliferation.