As the Uzbek Minister of Internal Affairs (between 1991 and the end of 2005), Almatov was responsible for the police. He is accused of having ordered the use of torture in pre-trial detention in prisons under his control. According to the UN Special Rapporteur on Torture, torture is systematically used in Uzbekistan.
Almatov is also believed to be responsible for the massacre on 13 May 2005 in Andijan. Security forces opened fire on a crowd of several thousand protesters, leaving hundreds dead or injured.
In December 2005, Almatov was receiving medical treatment for cancer in a specialised hospital in Hannover (Germany).
Human Rights NGOs and eight Uzbek citizens in December 2005 filed complaints against Almatov with the German general prosecutor and eleven alleged co-responsible persons („the devilish dozen“). They asked to open a criminal investigation.
On 16 December 2006, the UN Special Rapporteur on torture, Manfred Nowak, called on the German authorities to initiate a criminal investigation and prosecute Almatov.