A nine-minute clip titled, "Message to the People of Kyrgyzstan," urged people of Kyrgyzstan to move to the caliphate declared by the group in Iraq and Syria.
The video deleted hours later was picked up a Kyrgyz news site known for covering the activities of ISIS.
According to a statement issued on Monday by the State Committee for National Security (GKNB),
"All the relevant state organs are examining this video material."
Kyrgyzstan`s government designated ISIS as a terror group in March this year. It says more than 200 citizens are fighting with the group in Syria and Iraq.
The video clip was released days after Kyrgyz security services claimed they neutralised a cell of ISIS fighters in a deadly raid.
The video features an unnamed man speaking in Kyrgyz calling on citizens to "move from the country of infidels to the land of the Islamic State."
The speaker calls Kyrgyzstan, which is majority-Muslim, a country of "dishonour", living "according to laws made up by people, such as democracy."