Sheikh Abdullah bin Zayed said Abu Musa and the Greater and Lesser Tunbs were "an integral part of the territorial sovereignty of the UAE".
He condemned as a violation of international law Iran’s attempts to change their "legal, physical and demographic situation" since invading them on the eve on the UAE’s foundation in 1971.
In a wide-ranging speech to the General Assembly on Monday, Sheikh Abdullah also addressed the issues of Palestinian statehood, recent events in Bahrain, Libyan regime change, violence in Yemen and Syria and efforts to fight human trafficking and maritime piracy.
Supporting the Palestinian president Mahmoud Abbas’s application for full Palestinian membership of the UN, he said: "The UAE regards this legal step as complementing the pillars required for the establishing of the Palestinian state, and does not contradict the efforts of resuming peace talks."
The endorsement is largely symbolic as the decision on membership will be made by the Security Council. But added to broad support among UN members, it puts more pressure on the US, which has said it will veto the Palestinian bid.
Sheikh Abdullah said Israeli withdrawal from Palestinian territories in accordance with international resolutions remained a prerequisite to peace.
"The UAE condemns the continuous evasion by Israel of its international obligations … in particular Israel’s settlement policy in the Palestinian territories," he said. He further criticised Israel for violating Lebanese airspace and pursuing a nuclear programme without surveillance by the International Atomic Energy Agency.
Sheikh Abdullah condemned foreign interference in Bahrain. "While we are extending every required support to the government of Bahrain, we denounce any external intervention in Bahrain’s internal affairs," he said.
He encouraged Bahrain to pursue national dialogue, investigate alleged abuses by security forces and release prisoners.
On Syria, the minister called on the president, Bashar Al Assad, to "fulfil his recent commitments to stop military operations against Syrian civilians and carry out meaningful political reforms".
Sheikh Abdullah also spoke of the UAE’s participation in international efforts such as those in Libya, Afghanistan and Somalia, and in battling piracy.