It plans to issue "red notices" for the Iranians on March 31, unless either Iran or Argentina appeals the decision first, failing which the matter would be discussed at Interpol's general assembly in November.
"This shows that the Iranian regime has to co-operate in efforts to clarify this attack and not impede the search for the truth"
head of the Buenos Aires Jewish centre
Argentinian prosecutors have alleged that the attack was orchestrated by leaders of the Iranian government and executed by the Lebanon-based Hezbollah.
The six people on Interpol's list include Ali Fallahijan, the former Iranian intelligence chief.
Imad Moughnieh, a Lebanese, is also wanted for allegedly kidnapping Westerners in Lebanon in the 1980s, and suicide attacks on the US embassy and a US marine base in Lebanon which killed more than 260 Americans.
Iran has denied involvement in the bombing and said it would oppose any attempt to detain its citizens.
Luis Grynwald, head of the Jewish centre in Buenos Aires, which was rebuilt after the attack, hailed Interpol's move.
"The resolution by Interpol gives strong backing to the efforts of the prosecutor and the Argentine judiciary," Grynwald said.
"This shows that the Iranian regime has to co-operate in efforts to clarify this attack and not impede the search for the truth."
The three Iranians Interpol declined to issue red notices for are Rafsanjani, Ali Akbar Velayati, the former foreign minister and Hadi Soleimanpour, the former ambassador to Buenos Aires.
Mohsen Baharvand, an Iranian diplomat in Argentina, said the US was applying political pressure in the case.
He said Argentinian officials had no evidence to back warrants for the Iranians.
"The decision of Interpol is not acceptable for Iran," Baharvand said.
Iran and Argentina are Interpol members.
"Both parties have been treated fairly and impartially by Interpol"
Jackie Selebi, Interpol president
"Both parties have been treated fairly and impartially by Interpol, and the organisation's rules have been meticulously applied throughout the dispute resolution process," Jackie Selebi, Interpol's president, said.
A red notice is an Interpol request that a wanted person be arrested for possible extradition.
It cannot force countries to arrest or extradite suspects, but people with red notice status appear on Interpol's equivalent of a most-wanted list.