The move comes despite concerns by the UN's human rights chief Louise Arbour that the deportees could face torture in their home country.
Kyrgyzstan's prosecutor general Azimbek Beknazarov described the 29 deportees as "terrorists and criminals." He said the expulsion would take place within a week and would not be subject to what he called "any interference" from the UN refugee agency.
The office of the UN High Commissioner for Refugees in Bishkek did not comment on the latest developments but said it was "concerned" by the deportations.
Around 500 Uzbeks fled across the border from Andizhan to southern Kyrgyzstan on May 14, the day after police opened fire on a crowd of armed rebels and civilian protesters. The government said 173 people were killed, but opposition groups said up to 1,000 died.
Some information for this report provided by AFP and Reuters.