Mwanawasa faced an uphill battle from the moment of his inauguration. Bitter protests in Lusaka and the Copperbelt region over the outcome of the elections brought clashes with police before Mwanawasa was even inaugurated. He elected to extend the Christmas holiday recess at the University of Lusaka, where large protests following the election had brought university operations to a standstill. On 2 January 2002, Zambian judge Peter Chitenge rejected the petition by ten opposition parties to postpone Mwanawasa's inauguration and to force a ballot recount. Thousands of opposition protestors outside Chitenge's courtroom clashed with police as the verdict was announced. Although Mwanawasa's MMD party vigorously denied any vote-rigging, European Union observers monitoring the election process reported irregularities in the balloting.
Perhaps as part of an effort to convince his critics that he was his own man, Mwanawasa took bold action in the weeks immediately following his inauguration. He eliminated two of Chiluba's pet projects—the Presidential Housing Initiative and the Food Reserve Agency. Both were designed to benefit the poor but had accomplished little. He also fired Xavier Chungu, head of the secret service, and appointed a director from his home Copperbelt province to the post, lifting political restrictions on law enforcement. These moves surprised most Zambians, who had expected Mwanawasa to leave the Chiluba government in place, unaltered, since Mwanawasa was widely perceived to be Chiluba's puppet. However, in the early months of the Mwanawasa administration, key aides from the Chiluba era were being investigated for crimes ranging from corruption to murder. In March 2002, Mwanawasa launched an independent agency, National Movement Against Corruption, stating "Corruption is a crime against the nation and humanity for which punishment should be severe."
Early in 2003, Mwanawasa convened and appointed member to a Constitutional Review Commission charged with the task of forming a Constitution which would better serve the nation and reduce the conflict associated with the current document.