Mirziyoev told a meeting of the Prosecutor-General's Office and the MXX on January 31 that Inoyatov, who is 73 and led the MXX for almost 23 years, had been replaced by Ihtiyor Abdullaev, the officials said.
The officials spoke on condition of anonymity because they were not authorized to make public statements about the matter.
Inoyatov, who holds the rank of colonel general, was one of a relatively small number of senior officials who had retained their posts since the death of President Islam Karimov was announced in September 2016.
The MXX, the main successor of the Soviet-era KGB in Uzbekistan, is considered among the most closed and powerful agencies in the tightly controlled Central Asian country.
Inoyatov, who has avoided publicity and preferred to stay in the shadows, was one of the most influential officials in Uzbekistan for years.
When Karimov was dying after a quarter-century in power, many believed that Inoyatov would succeed him or, more likely, maneuver an ally into the presidency.
Abdullaev, 51, was the prosecutor-general until his appointment.
More about: Uzbekistan