Iran's Supreme Leader Ayatollah Ali Khameini said on Sunday the Islamic Republic may do away with popular elections for the presidency, Iran's semi-official Fars news agency reported Monday.

"Presently, the country's ruling political system is a presidential one in which the president is directly elected by the people, making this a good and effective method," Khameini said on state television.

"However, if one day, probably in the distant future, it is deemed that the parliamentary system is more appropriate for the election of officials (holding) executive power, there would be no problem in altering the current structure," Khamenei explained.

Khameini's comments are seen as a shot across the bow for protégé-turned-rival Mahmoud Ahmadinijad, and a warning to his possible successors in the 2013 elections not overstep the executive's limited prerogatives.

Ahmadinejad has battled constant criticism from hardliner conservatives who say he is in the thrall of "deviant" advisers seeking to undermine the role of the clergy, including the office of supreme leader.

While Ahmadinejad enjoyed Khamenei's full support when elected to a second four-year term in June 2009, analysts say an irreparable rift between the president and supreme leader emerged last April when Khameini overrode Ahmadinijad's move to dismiss his intelligence minister.

After the impasse the notoriously moody Ahmadinejad, long-linked to a movement of outré mystics predicting the imminent apocalyptic arrival of the Mahdi, refused to appear in public or perform his duties for eleven days.

Members of the conservative-dominated parliament have since threatened to impeach Ahmadinejad, and the judiciary has pursued some of his allies over corruption allegations.

Khamenei's comments have been seen as a none-too-subtle reminder of own paramount status in Iranian affairs over the presidency - as well as a rejection of the populist undercurrents of the so-called Arab Spring that Ahmadinijad has vocally supported.

Iran's 2009 elections saw immense crowds pour into the streets to protest the results, which they said were rigged. But hardliner elements loyal to Khameini and Iran's clergy brutally put down the protests before launching into the persecution of dissidents.

Ahmadinijad's reformist opponent, Mirhossein Mousavi, has been under unofficial house arrest since February and reformists have yet to say whether they will participate in the preliminary March 2012 elections – which will set the scene for the 2013 presidential race.

Public hangings of dissidents, as well the routine detention of high-profile opposition figures, have become the norm in Iran, where the Mullahs who seized power in 1979 seek to perpetuate their Islamic revolution.

While the supreme leader should not normally interfere in day-to-day political matters, Khamenei said, he had the responsibility to step in "under circumstances in which the adoption of a policy would lead to the diversion of the revolution's path".

Eliminating direct elections would, in the wake of popular uprisings that have shaken the region, potentially stave off a repeat of the 2009 protests and bring the presidency into lockstep with the conservative parliament and clergy.

Meanwhile, Khameini also warned the United States on Sunday that any measures taken against Tehran over an alleged plot to assassinate the Saudi ambassador to Washington would elicit a "resolute" response.

Two men, including a member of Iran's special foreign actions unit known as the Quds Force, have been charged in New York federal court with conspiring to kill the Saudi diplomat, Adel Al Jubeir.

"If US officials have some delusions, (they must) know that any unsuitable act, whether political or security, will meet a resolute response from the Iranian nation," Khameini told state television.

Khamenei's comments reflect Iranian concerns Washington will use the Al Jubeir case to ratchet up sanctions and recruit international allies to try to further isolate Tehran.