Iran’s intelligence minister was caught in the middle of a top level political dispute this weekend. After resigning from President Mahmoud Ahmadinejad’s government, Supreme Leader Ayatollah Ali Khamenei urged the man to say on. A majority of parliamentarians supported the religious leader’s appeal, forcing Ahmadinejad to reinstate the official.

The reason for the initial resignation remains unclear. It might be that the minister, who was instrumental in the violent crackdown of anti-government demonstrations following Ahmadinejad’s disputed reelection in 2009, disagreed with his president’s hardline policies. Or the move might be linked to possible intelligence failures when a powerful computer worm known as Stuxnet infiltrated Iran’s nuclear control systems and other industrial networks last year.

In any event, the latest episode illustrates Iran’s internal power struggle between Ahmadinejad and his powerful Revolutionary Guard who are moving the country toward military dictatorship on the one hand and the clergy and their conservative allies in parliament on the other.

Religious leaders and politicians from the older generation, who were part of the Islamic Revolution of 1979, fear that their president is squandering religious principles in favor of a messianic cult that rejects the intermediary role of the clergy. Ahmadinejad has referred to the divide among conservatives, warning that “the regime has only one party” while his supporters refer to the opposition as a “conspiracy” — the same rhetoric that was deployed against protesters in 2009.

The president’s office has come to favor a separation of Church and State with the executive as “the most important branch of government,” according to a statement last year that seemed to challenge the authority of the supreme leader and the Guardian Council which he elects.

Ali Khamenei is known as an ally of Ahmadinejad’s however and as fierce an antagonist of the West as his president. In a speech marking the beginning of the Iranian new year in March, the ayatollah praised the government for implementing bold economic reforms.

If not an all out dispute, Khamenei’s reinstatement of a cabinet member was at least an attempt at reasserting his political influence.

The supreme leader has traditionally approved the appointment of key ministers, including those charged with defense, intelligence and foreign affairs. Ahmadinejad’s unilateral and seemingly unexpected dismissal of one of these top officials may have overstepped his authority in the eyes of the ayatollah.