On 6 October 1999, he was promoted as four-star rank admiral and appointed Chief of Naval Staff after Admiral Bokharhi prematurely resigned from his commission in protest as the latter was denied the Chairmanship of Joint Chiefs of Staff Committee. Admiral Mirza remained supportive of martial law in 1999, and was said to be closer to Chairman joint chiefs and chief of army staff General Pervez Musharraf. Two weeks later, he was inducted as a senior member in the National Security Council alongside with Chief of air staff Air Chief Marshal PQ Mehdi. On 4 November 1999, Admiral Mirza released a report of his assets, with General Musharraf also releasing his tax returns papers. In 2000, Admiral Mirza notably announced of seeling the Agosta-90B Subamrines to Royal Saudi Navy and Royal Malaysian Navy but the agreement to sell the submarines were never materialized as Pakistan imposed an export restrictions.