"All of them agreed with the voluntary return and all of them boarded the plane. Everything went well," Christov told CTK.
The Iraqi group took a regular flight via Istanbul.
The Interior Ministry said the flight tickets cost about 100,000 crowns. The ministry will negotiate with the Generation 21 Endowment, which has organised the resettlement programme for Christians from Iraq, about its possible payment of the costs.
The endowment's head Jan Talafant said Generation 21 would pay the flight costs if it was possible. He said the administrative board of the endowment would deal with the issue.
The police detained the group of 16 Iraqi Christians, including children, on their way to Germany close to the Czech-German border last Thursday.
The group was granted asylum in the Czech Republic, but later they changed their mind and withdrew their asylum applications. After their detention, they applied for asylum in the Czech Republic again and were taken to a facility in Zastavka u Brna pending their asylum application is settled.
However, then they changed their mind again and applied for return to Iraq.
Another group of 20 Iraqis that left for Germany should be returned to the Czech Republic by the end of April.
The endowment has as yet brought 89 Christian refugees from Iraq to the Czech Republic.
The first to leave the country was a group of 25 people at the beginning of April who went to Germany. German authorities want to return 20 of them to the Czech Republic, while the remaining five-member family can stay as the father has already been granted asylum in Germany.
An eight-member Iraqi family left Brno for Iraq previously. The travels costs were covered by their relatives.
In reaction to the above groups' decision to leave the Czech Republic, the Czech government scrapped the Generation 21's project, which planned the resettlement of a total of 153 Iraqi Christian refugees, two weeks ago.
The project was scrapped a few days before the planned arrival of further two Iraqi families in the Czech Republic. Generation 21 said each family received 500 U.S. dollars in compensation as they already had flight tickets and sold their property.
Some 40 Iraqi Christians still stay in the Czech Republic. Talafant said no problem has occurred in these groups.