Ayatollah Ali Khamenei
Ayatollah Ali KhameneiReuters

Iranian Supreme Leader Ayatollah Ali Khamenei's top foreign affairs adviser revealed on Tuesday that despite the nuclear deal sealed last Tuesday, international inspectors will not be allowed to visit Iran's covert military sites that are said to house its secret nuclear weapons program.

The aide, Ali Akbar Velayati, was quoted by the semi-official Fars News Agency saying that world powers "have made some comments about defensive and missile issues, but Iran will not allow them to visit our military centers and interfere in decisions about the type of Iran's defensive weapons."

His statement raises concerns even higher over the complete absence of covert nuclear installations in the Iran deal, prime among them the Parchin military base where Iran has admitted to testing exploding bridge wire nuclear detonators.

Velayati also said that Iran will continue to produce domestic long-range ballistic missiles that are nuclear capable according to international reports, particularly the Shahab 3 and Sejjil 2.

"Missiles like Shahab, Sejjil and the like, have never been used for carrying nuclear warheads, and therefore, are not subject to the paragraphs of the Vienna draft agreement," said the adviser.

His comments echoed those of Iranian Foreign Minister Mohammad Javad Zarif, who on Tuesday told the Iranian parliament that "using the ballistic missiles doesn’t violate the Joint Comprehensive Plan of Action (JCPOA), and it is a violation of a paragraph in the annex of the (UN Security Council) Resolution (2231) which is non-binding."

"This paragraph (of the annex) speaks about missiles with nuclear warheads capability and since we don’t design any of our missiles for carrying nuclear weapons, therefore, this paragraph is not related to us at all," he said, playing down the capabilities of the rockets.

According to the deal a UN conventional arms embargo on Iran will end in five years, and sanctions against selling ballistic missiles to Iran will likewise expire in eight years.

Iran's nuclear program - military or "peaceful"?

At the core of the issue is Iran's claims that its nuclear program is peaceful in nature, a claim that has been debunked by the International Atomic Energy Agency (IAEA) in various reports indicating that sites like Parchin - which Iran has repeatedly rejected IAEA requests to inspect - have been used for nuclear weapons research.

IAEA chief Yukiya Amano announced last Tuesday that in addition to the nuclear deal, a "road map" agreement was sealed, by which Iran will disclose military aspects of its nuclear program by October 15. After this, Amano will write an assessment of Iran's claimed disclosures by December 15 "with a view to closing the issue."

Ali Akbar Salehi, head of the Atomic Energy Organization of Iran (AEOI), on Tuesday urged the IAEA to hurry its assessment and put behind the military aspects of Iran's program.

"Based on the agreement with...Amano, the issue with the PMD (Possible Military Dimension) should be resolved by December 15," Salehi said. "According to this agreement, the IAEA will present its report to the Board of Governors, while implementation of the Joint Comprehensive Plan of Action will continue separate from the results of this report."

Amano has said the "road map" agreement would include a visit to Parchin, but given Velayati's comments that prospect seems highly unlikely. Confirming that assessment, prior to the Iran deal Iranian officials rejected last-minute reports that inspections would be allowed at all covert sites.

Further raising doubts about a visit is the fact that satellite photos have shown Iran has been modifying Parchin, possibly expanding the nuclear tests and covering up their existence. Given that Iran will have 24 days before any inspection, it is likely that the leading state sponsor of terror would cover up evidence of nuclear weapons testing before IAEA inspectors arrive.