At the onset of military coup in October 1999, General Pervez Musharraf, a junior to Haider as he belonged to 29th PMA Long Course, put Haider as the Interior Minister of Pakistan. He continued to lead the powerful ministry till the 2002 October elections, when Faisal Saleh Hayat replaced him. During his time as Interior Minister he was very involved in hunting down and bringing to justice the killers of American Wall Street Journal reporter Daniel Pearl.