Domestic issues

Shortly after Musharraf's takeover, several people filed court petitions challenging his assumption of power. However, he got The Oath of Judges Order 2000 issued. It required the judges to take a fresh oath of office swearing allegiance to military rule and to state they would make no decisions against the military. Many judges refused and resigned in protest. On 12 May 2000, the Supreme Court asked Musharraf to hold national elections by 12 October 2002; elections for local governments took place in 2001.

In an attempt to legitimize his presidency and assure its continuance after the approaching restoration of democracy, he held a referendum on 30 April 2002 to extend his term to five years after the October elections. The voter turnout was 80 percent by most estimates, amidst claims of irregularities. A few weeks later, Musharraf went on TV and apologized to the nation for "irregularities" in the referendum.

In August 2002, he passed the Legal Framework Order which provided for the general elections of 2002 and the revival of the 1973 Constitution, but added numerous amendments to the Constitution. The Supreme Court rejected part of the Order.

General elections were held in October 2002 and a plurality of the seats in the Parliament was won by the Pakistan Muslim League (Q) (PML-Q), a pro-Musharraf party. It formed a majority coalition with independents and allies such as the Muttahida Qaumi Movement (MQM). However, parties opposed to Musharraf effectively paralysed the National Assembly for over a year. The following month, Musharraf handed over certain powers to the newly elected Parliament. The National Assembly elected Mir Zafarullah Khan Jamali as Prime Minister, who in turn appointed his own cabinet.

In December 2003, Musharraf made a deal with Muttahida Majlis-e-Amal, a six-member coalition of Islamic parties, agreeing to leave the army by 31 December 2004. With that party's support, pro-Musharraf legislators were able to muster the two-thirds supermajority required to pass the Seventeenth Amendment, which retroactively legalized Musharraf's 1999 coup and many of his decrees. In late 2004, Musharraf went back on his agreement with the MMA and pro-Musharraf legislators in the Parliament passed a bill allowing Musharraf to keep both offices. Constitution Article 63 clause (1) paragraph (d), read with proviso to Article 41 clause (7) paragraph (b), allows the President to hold dual office.