If Iran signs a nuclear deal with world powers it will have to accept inspections of its military sites, the head of the UN's atomic watchdog Yukiya Amano told AFP in an interview.

The question of inspections is shaping up to be one of the thorniest issues as world powers try to finalise a deal by June 30 to prevent Iran from developing a nuclear bomb.

Amano said Tehran has agreed to implementing the Additional Protocol of the Nuclear Non-Proliferation Treaty (NPT) that allows for snap inspections of its nuclear facilities, and if required, military sites.

However, differences have emerged over the interpretation of the protocol and the issue is far from resolved.

Iran's supreme leader Ayatollah Ali Khamenei last week ruled out allowing nuclear inspectors to visit military sites or the questioning of scientists.

And Foreign Minister Mohammad Javad Zarif has said the protocol allows "some access" but not inspections of military sites, in order to protect national "military or economic secrets".

In an interview with AFP and French daily Le Monde, Amano said that if a deal is reached, Iran will face the same inspections from the International Atomic Energy Agency (IAEA) as any of the 120 countries implementing the additional protocol.

"When we find inconsistency or when we have doubts we can request access to the undeclared location for example, and this could include military sites," said the Japanese diplomat.

"Some consideration is needed because of the sensitiveness of the site, but the IAEA has the right to request access at all locations, including military ones."

Iran and the so-called P5+1 group -- Britain, China, France, Russia, the United States plus Germany -- have been engaged for nearly two years in negotiations on Tehran's nuclear drive.

The deal is aimed at preventing Iran from developing the atomic bomb in exchange for an easing of crippling economic sanctions.

The two sides signed a framework agreement on April 2 and began meeting in Vienna on Wednesday to start finalising a deal which is due by June 30.

- Possible military dimension -

Iran has long asserted its nuclear programme is for peaceful energy purposes, and that international concern about it seeking a nuclear bomb is misplaced.

According to the United States, Iran has agreed to cut the number of its centrifuges, used for enriching uranium, by two thirds from 19,000 to about 6,000, and will put excess nuclear equipment into storage monitored by the IAEA.

Iran has also reportedly agreed not to build any new facilities for enriching uranium for 15 years, cut back its stockpile of enriched uranium and mothball some of its plants.

However, Tehran is sensitive over the IAEA's stringent oversight demands as the agency is at the same time trying to probe allegations that Iran tried to develop nuclear weapons prior to 2003, and possibly since.

Iran denies the allegations, saying they are based on hostile intelligence provided by the US Central Intelligence Agency (CIA) and Israel's Mossad.

Western officials stress that these claims of "possible military dimensions" need to be cleared up before sanctions can be lifted, but the IAEA's probe has been stalled since last August.

- 'A huge operation' -

Amano said that once there is a deal, "several months will be needed" to investigate whether there were any military dimensions to Iran's research.

"It depends very much on the pace and the intensiveness of the cooperation from Iran. We have identified 12 areas to clarify."

One notable area the IAEA is interested in is the Parchin military base, where they suspect tests relating to the development of nuclear weapons have taken place.

The IAEA has already visited the sprawling military base near Tehran but wants to return for another look.

Amano said it could take years "to give the credible assurance that all activities in Iran have a peaceful purpose".

If a deal is reached with the P5+1, the IAEA will be charged with overseeing it and reporting back to the UN Security Council.

"This will be the most extensive safeguard operation of the IAEA. We need to prepare well, we need to plan well, it is a huge operation," said Amano.

Currently the watchdog has between four and 10 inspectors in Iran at any given time, and if a deal is reached at least 10 will need to be on the ground daily.

The agency will also need to install cameras and seals on sensitive equipment.