Kosovo Prime Minister Ramush Haradinaj has sacked two top security officials for failing to tell him about the arrest and deportation of six Turks.
Turkey says the six support Fethullah Gulen, the US-based cleric blamed by Turkish President Recep Tayyip Erdogan for a plot to oust him in 2016.
Mr Haradinaj and Mr Erdogan have both said the six were sent back on Thursday.
It is reported to be Europe's first deportation of "Gulenists" to Turkey.
Several hundred such suspects have been sent back to Turkey previously from outside Europe, from countries such as Sudan, Pakistan and Afghanistan, the Turkish daily Hurriyet reports.
Most of Kosovo's population is ethnic Albanian and Muslim.
Since breaking away from Serbia in 1999, Kosovo has forged close ties with Turkey, getting much-needed economic assistance. Turkish firms run the airport and electricity network.
Mr Haradinaj sacked Kosovo Interior Minister Flamur Sefaj and intelligence agency chief Driton Gashi.
In a tweet, he said he had not been informed about the Kosovo Intelligence Agency operation.
Five of the suspects are teachers at schools run by the Mehmet Akif College, a Kosovo-based institution reported to have links to Mr Gulen. On Thursday college students demonstrated against their arrest.
Hurriyet, quoting security sources, said all six had been detained by Kosovo officials on Thursday "as a result of co-operation" between the two governments.
They were later taken to the airport near the capital, Pristina, and handed over to Turkish intelligence officials, Hurriyet said.
Mr Erdogan has cracked down hard on alleged Gulen supporters, arresting or dismissing thousands of public servants, and urging foreign governments to hand over suspects.