Cyprus said that the contents of the English textbook were "completely inappropriate and unacceptable".
ADVERTISEMENTSchools in Cyprus have been ordered to remove a textbook praising the founder of modern Turkey.
The Cypriot education ministry said an English book lauding Mustafa Kemal Atatürk had been removed from the curriculum.
In a leaked email, the ministry asked secondary school teachers to "tear out page 36 before giving it to students," after public criticism.
The page in question had referred to Atatürk as "Turkey's greatest hero". Cyprus later decided the remove the textbook altogether.
Turkey has "strongly condemned" the decision and accused Cyprus of hostile actions.
The two countries have had tense relations since Turkish forces invaded the island in response to a coup by supporters of a union with Greece in 1974.
Since then, the EU member state has been divided along ethnic lines, between the Republic of Cyprus from the self-proclaimed Turkish Republic of Northern Cyprus.
In a statement on Wednesday, Cyprus' education ministry said it was "not possible" to accept textbooks that praised Atatürk.
"Atatürk's name is directly associated with crimes against humanity such as the Armenian genocide, which is unequivocally condemned by our country, the US, France, and many others," the ministry added.
"The modern school, which is based on respect for human rights and the rights of peoples, does not compromise with attempts to embellish such historical crimes."
"For these reasons, the book, in view of this completely inappropriate and unacceptable - even regional - excerpt, is deemed inappropriate and is temporarily withdrawn until a solution is given."
In a further statement on Thursday, Cyprus acknowledge that books praising can be circulated among the population but should not be used in schools.
"Neither the Turkish Foreign Ministry nor the Turkish administration in the occupied territories can have a say in the matter," the ministry added, denying allegations of "censorship".
On Wednesday, Turkey's Foreign Ministry had released its own statement criticising the decision.
"We strongly condemn this outdated, hostile, and unacceptable attitude of the Greek Cypriot Administration," Ankara said.
"This latest action of the Greek Cypriot Administration ... shows that they have no patience to not only share power and prosperity but even live together with the Turkish Cypriots on the Island."
Niyazi Kizilyurek, the only Cypriot-Turkish MEP in the European Parliament, also denounced the measure.
"Unfortunately, in both [Cypriot] communities, the education sector is anachronistic, and with these interventions, it becomes even worse," he added.
ADVERTISEMENTOfficially the entire territory of the island of Cyprus has been considered EU territory since 2004.