"Comments made about the Iranian islands in the Persian Gulf are neither right nor well-considered," foreign ministry spokesman Ramin Mehmanparast told Mehr news agency.
"With cooperation within the Islamic world in mind, we have always sought to warn against the main threat in the region which is the regime occupying Al-Quds (Jerusalem)," he said alluding to Israel.
"Misunderstandings between friends can be resolved through bilateral talks," he said, while calling on United Arab Emirates (UAE) leaders to "avoid comments which benefit the Zionists."
On Tuesday, Emirati Foreign Minister Sheikh Abdullah bin Zayed al-Nahayan likened Iran's control of the three strategic islands in the southern Gulf to Israel's occupation of Arab territories.
Iran, under the rule of the Western-backed shah, gained control of the islands in 1971, as Britain granted independence to its Gulf protectorates and withdrew its forces.
The Islamic republic took possession of the the Lesser and Greater Tunbs, while a third, Abu Musa — the only inhabited island — was placed under joint administration in a deal with Sharjah, now part of the UAE.
But the UAE says the Iranians have since taken control of all access to the strategic island and installed an airport and military base on Abu Musa.
The UAE, facing Iran across the Gulf waterway vital for world oil supplies, has a large Iranian expatriate community and is a major conduit for Tehran's trade with the outside world.
