The committee said it drew the conclusion from citizens' nationality rather than polls or census.
"As on February 5, 2013, Tajikistan had a population of eight million. Judging by nationality, 7,952,000 are Muslims and 48,000 belong to other religions," the committee said.
"Hence, Muslims amount to 99.4% of the entire population," it said.
The committee referred to the nationality data presented by the Tajik Statistics Agency.
Apart from Hanafi Sunni Muslims, Tajikistan has over 200,000 Ismailite Shiite Muslims. The country has 74 non-Islamic religious organizations. The precise number of atheists and non-Islamic believers is unknown. Yet some ethnic Tajiks and people of other traditionally Islamic nationalities go to Orthodox, Adventist or Baptist churches.
Tajikistan has 3,712 mosques, three medrasahs (Islamic general education schools) and the Islamic University.