'When a government doesn't take shape within the framework of the law, it has no legitimacy in the eyes of the people. This weakens the government and encourages the government to resort to violence against the people,' The Star Online quoted Mousavi, as saying.
Iranians have begun to cast their votes in the country's closely-fought presidential election.
Iranian President Mahmoud Ahmadinejad, known for his frequent run-ins with the West, is seeking a second four year term.
State television quoted Khamenei directing the Guardian Council to look into charges by Ahmadinejad's rival and pro-reform candidate Mir Hossein Mousavi.
Azadi Square in central Iran witnessed the country's biggest protest in over three decades when thousands turned up to condemsn the alleged rigging of the recent presidential elections.
A video posted on YouTube on Tuesday appears to show riot police flooding the streets of Teheran in an attempt to disrupt large-scale protests in the wake of Iran's disputed presidential election, FOX News reports.
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