There were anti-government protests led by lawyers, who have spearheaded a campaign against Musharraf in recent months in the four provincial capitals - Karachi, Lahore, Peshawar and Quetta.
Police fired tear gas to disperse lawyers pelting rocks at the North West Frontier Province assembly, and the lawyers also threw a burning effigy of the president on top of an armoured police vehicle.
The ruling coalition's majority should ensure that Musharraf beats his two rival candidates.
However, his position will remain uncertain until October 17 - when the court is due to reconvene.
Wajihuddin Ahmad, a former judge who refused to swear allegiance to Musharraf after the coup that brought him to power in 1999, and Makhdoom Amin Fahim, the vice-chairman of Benazir Bhutto's Pakistan People's Party, have no hope of securing the votes to give them victory.
"I am fully confident that the supreme court will give a balanced judgment," Musharraf said during a telephone interview on Pakistan Television.
Musharraf emphasised the court's recognition of his re-election rights by the current parliament.
|Makhdoom Amin Fahim is the candidate for|
the Pakistan People's Party [AFP]
If re-elected for another five-year term the president has promised to leave his position as head of the army by November 15 and be sworn in as a civilian leader.
Azeem said the government "respects" the supreme court decision.
He said: "It would have been better if they had given a final verdict and put the whole issue and legal wrangling to bed."
Musharraf has been in conflict with the supreme court since he attempted to sack Iftikhar Muhammad Chaudhry, the chief justice, sparking mass protests.
Opposition parties have vowed to stage protests over Musharraf's decision not to step down from his army post ahead of the election.
More than 160 assembly members, many belonging to an opposition alliance led by Nawaz Sharif, the former prime minister, who was ousted by Musharraf, have already resigned.
"Pakistan needs a military leader who can control both civil and possible military extremism"
Creative_person01, Islamabad, Pakistan
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But Musharraf has averted a walk-out by Bhutto's PPP by granting her amnesty from corruption charges, paving the way for a power-sharing deal between the two politicians.
Bhutto, whose party is the country's largest, had earlier threatened to further undermine Musharraf's widely anticipated victory by pulling her MPs from parliament, after other opposition parties also resigned.
The amnesty clears the way for her planned homecoming on October 18 in the run-up to parliamentary elections due by early 2008.