Abd al-Rahman Hamad al-Attiya, secretary-general of the Gulf Co-operation Council, said the Lebanon-Syrian crisis would also be discussed at the two-day summit being held in the United Arab Emirates capital, Abu Dhabi.
Leaders from the six GCC states have been watching with concern the West's increasing confrontation with Iran over its nuclear ambitions - exacerbated by recent anti-Israeli comments by Iran's president.
They also have their own fears about Iran's nuclear programme - particularly that with a nuclear arsenal, Tehran would push its attempts to become the superpower in the Gulf.
The issue was weighing heavily on the summit that was officially opened on Sunday by Shaikh Khalifa bin Zayed al-Nahyan, the president of the Emirates.
"We want Iran to be logical in dealing with the nuclear issue, in such a manner that it meets its peaceful purposes without inflicting damage on its neighbours," al-Attiya was quoted as saying by the official Emirates News Agency.
Iran denies US allegations that it
seeks to produce nuclear weapons
"We have confidence in Iran, but we don't want to see an Iranian nuclear reactor that is closer to our territorial waters than it is to Tehran. This causes danger and harm to us."
The Gulf leaders will consider an initiative to declare the region "free of nuclear weapons and weapons of mass destruction", then to seek to persuade Iran, Iraq and Yemen to join, al-Attiya said.
The GCC summit will not issue any statements condemning Iran's nuclear programme, he said.
That reflected the Gulf nations' reluctance to provoke Iran and seeming to side with the West.
The United States accuses Iran of seeking to produce nuclear weapons, a charge Iran denies, saying its programme is intended only to produce electricity.
The GCC, formed in 1981, has
not achieved much of its goals
GCC leaders will also discuss the Lebanese-Syrian situation, al-Attiya told reporters.
He condemned the spate of bombings in Lebanon, the most recent being an attack on Monday that killed Gebran Tueni, a Lebanese legislator and anti-Syrian journalist.
Many Lebanese have blamed Syria for being behind the blasts.
UN investigators have implicated Syrian and Lebanese security officials in the assassination in February of Rafik al-Hariri, the former Lebanese prime minister. The killing sparked massive protests and the withdrawal of Syrian soldiers from Lebanon in April.
GCC member Saudi Arabia has been among key countries persuading Syria to co-operate fully with the United Nations Security Council-ordered investigation into the bombing that killed al-Hariri and 22 others.
The leaders of the GCC countries - Saudi Arabia, Oman, Bahrain, Qatar, Kuwait the United Arab Emirates - will hold at least one closed session in addition to bilateral meetings during the two-day event dubbed the Fahd Summit in honour of the late King Fahd of Saudi Arabia, who died in August.
The GCC is a loose military and political alliance that was formed in 1981 to devise a unified political, economic and military policy.
However, it has achieved little and disputes have often developed between members states.
Also on the agenda is the issue of a unified market and a monetary union.