Secretary of State John Kerry raised the matter in a phone call with the Russian Foreign Minister, Sergey Lavrov, the White House said.
Russia said the embargo was no longer necessary after an interim deal was reached on Iran's nuclear programme.
Tehran and six world powers aim to reach a final deal by 30 June.
White House spokesman Josh Earnest did not give details of Mr Kerry's phone call, but said that "coordination and unity" with nations like Russia had been key to reaching agreement with Iran.
A Pentagon spokesman called the move "unhelpful", saying concerns were being raised through the "appropriate diplomatic channels".
Russia agreed to sell the S-300 system in 2007, but blocked delivery in 2010 after the UN imposed sanctions on Iran over its nuclear programme.
The S-300 is a surface-to-air missile system that can be used against multiple targets including jets, or to shoot down other missiles.
Tehran welcomed the move as a step towards "establishing stability and security in the region", the country's Defence Minister Hossein Dehghan said, according to state media.
But Israel, a vocal critic of the nuclear deal, has voiced dismay.
"This is a direct result of the legitimacy that Iran obtained from the emerging nuclear deal,'' said Intelligence Minister Yuval Steinitz.
Mr Lavrov said the "S-300 is exclusively a defensive weapon, which cannot serve offensive purposes and will not jeopardise the security of any country, including, of course, Israel".
It is not clear when the systems will be delivered. Russia has stopped producing the model specified under the original contract and has instead offered an upgrade.
The deal on Iran's nuclear programme aims to restrict its ability to make nuclear weapons in exchange for sanctions relief.
It is due to be finalised by the end of June deadline, but sticking points remain, in particular on how and when to lift sanctions
Mr Kerry meanwhile has been holding closed door briefings with the US Congress, as he seeks to win over sceptical lawmakers who have threatened to block the deal.
The US has expressed concern after Russia lifted a ban on supplying Iran with the sophisticated S-300 air defence missile system.