Mahfud was appointed as Minister of Defense by President Abdurrahman Wahid on 23 August 2000. The appointment of Mahfud as the Minister of Defense caused controversy, after being rumored that the appointment was disagreed by vice president Megawati Sukarnoputri, although Mahfud later admitted that he met Megawati in personal, and confirmed that she didn't have any problems with his appointment. Following a cabinet reshuffle on 20 July 2001, Mahfud moved from the defense portfolio and was appointed Minister of Justice and Human Rights. He held office briefly until Wahid's impeachment by the People's Consultative Assembly a few days later and the Mutual Assistance Cabinet's formation.
2004 Parliamentary Elections
In 2004, Mahfud became one of the National Awakening Party's nominees for the 2004 parliament election. He was successful in the elections and become a member of the People's Representative Council for the term of 2004–2009. He sat on a number of parliamentary commissions during his term in parliament.
Constitutional Court Judge
In 2008, Mahfud selected as one of the constitutional judges. In the Indonesian Constitutional Court election for chief justice, he narrowly defeated the incumbent Jimly Asshiddiqie to become the second chief justice of the court. He ultimately resigned from parliament upon taking office. He served in the position until his term ended in April 2013. Mahfud attracted considerable publicity during his period at the court. The court is regarded as having made some progressive decisions and transformed the Constitutional Court being free of corruption during his time as chief justice but has also issued some surprising decisions such as an unexpected ruling in late 2012 that the existence of the upstream oil and gas regulatory agency BPMigas was unconstitutional.
Mahfud has been married to Zaizatun Nihayati since 1982. The couple has three children, Ikhwan Zein, Vina Amalia, and Royhan Akbar. Mahfud is well known as a commentator and public speaker. He often comments on issues concerning human rights in Indonesia. His comments, for example about the rights of atheists and communists under Indonesian law caused a fuss in mid-2012 when he said people could only be punished for being atheists or communists if they behaved in a way that breached the national ideology of Pancasila. More recently, in September 2012 he was critical of a proposal from the National Counterterrorist Agency to certify Islamic clerics and scholars as a way of minimising the risk of radicalism. Towards the end of 2012 there was increased speculation about the possibility that Mahfud would become a candidate in the 2014 presidential elections in Indonesia. Several polls indicated high support for Mahfud amongst some groups of voters. In November 2012 he stood for, and was elected to, the position of chair of the Islamic Students Alumni Association, an influential Muslim organisation. His decision to successfully seek election as the chair of KAHMI, and being selected ahead of other well-known politicians such as Anas Urbaningrum, was seen as boosting his credibility as a potential presidential candidate.