Mammadov was deputy chief commander of Leningrad Military District before he was invited to lead the Ministry of Defense in Azerbaijan. On September 2, 1993 acting PresidentHeydar Aliyev appointed Mammadov the Minister of Defense of Azerbaijan. He was appointed to the post at powerful colonel Suret Huseynov's request when Aliyev assumed power in June 1993, mainly because of his close ties to Russian military officials, including the Russian Defense Minister, Pavel Grachev, in the hope that closer military ties with Russia would benefit Azerbaijan. However, the connections yielded the opposite. During his official visit to Russia in 1994, Mammadrafi Mammadov agreed to station two regiments of Russian armed forces in Azerbaijan which was announced by Grachev during the joint press conference. Since the motion was not previously communicated to and approved by President Aliyev, the claims were immediately refuted by outraged Aliyev himself. Within the next few months, Grachev as well as Anatoly Kornukov travelled to Azerbaijan to persuade Azerbaijani authorities to allow Russian military presence in Azerbaijan but were denied the requests. However, Mammadov is also credited for notifying Baku authorities of acts of sabotage in Azerbaijan. While working in Moscow, Mammadrafi Mammadov passed confidential information about planned helicopter attack of Russian forces on the dissolved Soviet military base in Ganja which was to transfer considerable amount of ammunition and equipment to Azerbaijan as per agreement between Russian and Azerbaijani authorities. The warehouses were immediately emptied and equipment was saved. Throughout Mammadov's term in office, most of Azerbaijani territories were not recaptured and remained under Armenian military control. Mammadov was one of the co-signers of Bishkek ceasefire agreement. After the war, he also tried to arrange a 3,500 Germanpeacekeeping force on Karabakh frontlines under auspices of the Organization for Security and Co-operation in Europe. On February 6, 1995 Aliyev removed Mammadov from his post, replacing him with Colonel GeneralSafar Abiyev.
