Earlier this month, the Kyrgyz State Committee for National Security, the Kyrgyz Prosecutor-General's Office and the State Directorate for Religious Issues filed a complaint with the court.
In it, the state bodies claimed the church's activities posed a threat to Kyrgyz national security by forcibly propagating nontraditional religious views without proper registration.
The Unification Church became active in the former Soviet Union in the 1990s and has thousands of followers in the region.
Religious authorities in a number of post-Soviet states, including Russia, have harshly criticized the movement, calling it a sect.
Some curbs have been imposed on the Unification Church in those places as a result.
The Unification Church was founded in South Korea in 1954 by Sun Myung-moon, whom followers consider to be a messiah.