Almatov had been a focus of international criticism for his handling of protests in the eastern Uzbek city of Andijon in May, during with Uzbek troops opened fire on protesters.
Uzbek officials put the death toll at 187 people, most of them militants, police, and soldiers. Tashkent maintains that troops acted to quell an uprising by Islamic militants following a prison break.
International human rights organizations say, however, that troops fired indiscriminately into a crowd mainly comprising unarmed demonstrators who were demanding an end to a trial against local businessmen. They believe many hundreds were killed.
Almatov has in recent days been in the international spotlight after the UN’s special rapporteur on torture, rights organizations, and relatives of Andijon victims called on Germany to prosecute Almatov. Almatov was exempted from an EU travel ban on senior Uzbek officials in order to undergo life-saving medical treatment in Germany. Almatov quickly left hospital when the possibility of charges were raised. His current whereabouts are unknown.
The new interior minister will be Anvar Salihbaev. He too is named in the list of Uzbek officials banned from entering the European Union.