The declaration of a federation in northern Syria would be an invalid unilateral move, said a Turkish Foreign Ministry official on Wednesday, following a statement by a high-ranked PYD representative.
The United States also announced it would not recognise any self-ruled, semi-autonomous zones in Syria, State Department spokesman Mark Toner said on Wednesday.
Idris Nassan from the PYD-controlled city of Kobane on the Turkish-Syrian border said earlier that Kurdish-controlled areas in northern Syria will form a federal system.
He said the system would be named "the Federation of northern Syria," and would represent "all ethnic groups" living there.
Reiterating Turkey’s support for the unity of Syria, the Turkish official said such a move would not be valid and would not be welcomed by Turkey.
He also said all sections of Syria should take part in forming a new government and administrative structure in the country with a new constitution.
The activities of the YPG, which is the armed wing of the PYD, have been questioned by internationally due to the group's attitudes towards non-Kurdish ethnic groups, including Turkmen and Arab minorities living in the region.
In mid October last year Amnesty International said in a report that YPG militants had committed war crimes by forcing thousands of non-Kurdish civilians out of their homes and demolishing entire villages.
The London-based rights watchdog released a report on Tuesday in which it said more than a dozen villages were destroyed by the PYD, which is supported by the United States in the fight against DAESH.
"By deliberately demolishing civilian homes, in some cases razing and burning entire villages, displacing their inhabitants with no justifiable military grounds, the Autonomous Administration is abusing its authority and brazenly flouting international humanitarian law, in attacks that amount to war crimes," said Lama Fakih of Amnesty International, who undertook the research.
"In its fight against IS [DAESH], the Autonomous Administration appears to be trampling all over the rights of civilians who are caught in the middle," Fakih said.
"This report uncovers clear evidence of a deliberate, co-ordinated campaign of collective punishment of civilians in villages previously captured by IS [DAESH], or where a small minority were suspected of supporting the group."
More dramatically, some civilians were threatened by YPG militants with US-led air strikes if they failed to leave their homes, according to the report.
"They told us we had to leave or they would tell the US coalition that we were terrorists and their planes would hit us and our families," said one of the residents quoted in the report.
YPG militants took control of the area in February with the support of US-led air strikes and heavy weapons given by the US. Since then the militants have been demolishing villages and displacing villagers with majority Arab and Turkmen populations.