In 1928, Muhammad Ali went to join the Indian Civil Service, first working as an accountant at the Audit and Accounts Service and was deputed to audit the Bahawalpur state. In 1936, Muhammad Ali was moved as Private Secretary to James Grigg, the Finance minister of India, who later appointed him as the First Indian financial adviser when Grigg was appointed as the War Secretary in 1945. In 1946-47, Muhammad Ali was selected to serve as one of two secretaries to the presided over by Lord Mountbatten, later appointed as Finance Secretary at the Ministry of Finance. Over this issue of partition, Muhammad Ali worked with H.M. Patel and Walter Christir to prepare a document titled "The Administrative Consequences of Partition".