He said the Interior Ministry will discuss the covering of the return costs with the Generation 21 Endowment that brought them to the Czech Republic earlier this year.
The police detained the group on their way to Germany close to the Czech-German border on Thursday.
The group, including children, was granted asylum in the Czech Republic, but later they changed their mind and said they will go to Germany. 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.
Chovanec told Czech Television on Tuesday that he does not know the reasons for the Iraqis' change of mind.
"They probably realised that their possibilities to travel to other countries are very limited. Now, they would be waiting in the Czech Republic for whether they will again gain international protection and that is why they decided not to use this and return home," Chovanec said.
He said the state will secure the cheapest air transport to Iraq for them because it will pay for it. "I would be very glad if Generation 21 paid it because the state did not cause the problem," Chovanec said.
Jan Talafant, director of the endowment, told CTK that he does not know the reasons why the Iraqis decided to return home.
He said it would be fair if they paid for the transport by themselves.
The Iraqis were returned their passports by the Interior Ministry on Thursday and asked for their asylum status to be ended. They were given three days to leave the EU.
They left for Germany on a minibus of a private company.
The Interior Ministry says it told them that they must not illegally cross the border of any other EU country and that the departure order meant they must leave the EU.
On Thursday evening, their minibus was halted by the police in north Bohemia some eight kilometres from the German border. The police suspect the two drivers of people smuggling.
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 from Okrouhlik near Jihlava, south Moravia, at the beginning of April. They went to Germany. German authorities want to return 20 of them to the Czech Republic. The remaining five-member family will not return because the father has already been granted asylum in Germany.
One week ago, an eight-member family left Brno for Iraq, saying they are homesick.
Generation 21 wants to continue taking care of the remaining 40 refugees whose stay in Prague and Sobesovice in the Moravia-Silesia Region minimally throughout the first year of their stay in the Czech Republic.
In reaction to the above groups' decision to leave the Czech Republic, the Czech government scrapped the Generation 21's programme that planned the resettlement of a total of 153 Iraqi Christian refugees, two weeks ago.