The ministry says it considers the evacuation as "inadmissible and outrageous interference by foreign forces."
In May, hundreds of Uzbeks fled into Kyrgyzstan after an uprising and a government crackdown that one UN report described as a "mass killing."
Uzbekistan says 187 people -- mostly Islamic militants -- were killed. Rights advocates fear the death toll was much higher, and included civilians.
The evacuation was conducted after UN and international human rights groups expressed concerns that the refugees could be tortured or executed if handed over to Uzbek authorities.
For RFE/RL's full coverage of the Andijon violence and its aftermath, see "Unrest In Uzbekistan"