Botakoziev, 42, has not been seen since February 26 when he was at the UN High Commissioner for Refugees (UNHCR) office in Dushanbe applying for refugee status.
Botakoziev had applied for UNHCR protection after reportedly being repeatedly harassed by police in the southern Kyrgyz town of Nookat since 2004.
He said he was being persecuted by the police because of issues related to his Uzbek wife, Mavlyuda Abdulazizova, who had been sentenced more than a decade ago in Uzbekistan on charges of attempting to overthrow the government.
She was pardoned in July 1999 and fled to Kyrgyzstan, where she met and married Botakoziev.
In September 2008, Nookat residents attacked the local administration building to protest an official refusal to allow a public celebration of the Muslim holiday of Eid. Botakoziev was accused of organizing the protest and a warrant was issued for his arrest. He fled to Tajikistan and denies any involvement in the protest.
Botakoziev was also an associate of Kyrgyz journalist Alisher Saipov, who was shot dead in the southern Kyrgyz city of Osh in 2007.