The resolution, the first against Tehran in almost four years, was passed by a 25-3 margin, with six abstentions, by the 35-nation governing board of the International Atomic Energy Agency (IAEA) in Vienna.
The move received rare Russian and Chinese backing but it was unclear whether the measure would translate into support from Beijing and Moscow for further sanctions that Western leaders may push for if Iran does not begin to dispel concerns about its nuclear ambitions soon.
Most developing nations on the IAEA board opposed the resolution, which was sponsored by Britain, France, Germany, China, Russia and the United States, saying it would be provocative and counterproductive.
The resolution criticises Iran for defying a UN Security Council ban on uranium enrichment.
It also rebukes Tehran for secretly building a uranium enrichment facility near the city of Qom.
Supporters of the resolution were provoked by the revelation in September of the site, which Iran had been building for at least two years.
The discovery of the site has fuelled suspicions among Western states that Iran could be building other covert facilities dedicated to the making of nuclear weapons.
The resolution notes that the IAEA cannot confirm that Tehran's nuclear programme is exclusively geared towards peaceful uses and expresses "serious concern" that Iran may be hiding a military nuclear program.
Iran, which says its nuclear activity is for peaceful purposes, had warned before the vote that passing the resolution would undermine its relations with the IAEA.
The measure also signalled that IAEA members hare losing patience with Iran's reluctance to fully accept an IAEA-brokered plan to provide it with fuel for a nuclear medicine reactor, in exchange for enriched uranium that could be turned into bomb material if further refined.
On Thursday, Mohamed ElBaradei, the director-general of the IAEA, said an investigation into whether Iran was seeking to build nuclear weapons had reached "a dead end".