A Turkish Foreign Ministery on Wednesday said Barzani's appointment even before Iraq could draw up a new constitution outlining the country's new administrative system, made little sense.
The spokesman also stressed that the protection of Iraq's political unity and territorial integrity were necessary for its own national interests and the well-being of the region.
Former rebel leader Barzani took oath of office on Tuesday to become the first president of Iraqi Kurdistan.
Ankara apprehends that an assertive Iraqi Kurdistan could spur a separatist movement among its own minority Kurd population.
"I promise to safeguard the accomplishments of Kurdistan and to carry out my duties faithfully," Barzani told MPs and dignitaries gathered at the autonomous region's parliament in the northern city of Arbil.
Barzani took his oath of office at
Arbil's Iraqi Kurdish parliament
Barzani took his oath of office under a massive portrait of his father, nationalist hero Mullah Mustafa Barzani, framed between large red, white, yellow and green Kurdish flags.
He told the assembly and guests from the national parliament that their presence showed "the strength of Kurdish-Arab relations and the broad brotherhood among Kurds, Arabs, Turkmen and others".
While some Kurds still seek full independence, Barzani's Kurdistan Democratic Party and Iraqi President Jalal Talabani's Patriotic Union of Kurdistan have dropped such claims, settling instead for a federal Iraq.
Most Iraqi Kurds are Sunni Muslims and make up nearly 20% of Iraq's 26 million population.
However, the status of the northern oil hub of Kirkuk is a bone of contention after it was heavily Arabised under former president Saddam Hussein.
The city is rife with ethnic tension between Kurds, Arabs and Turkmen, with Kurds insisting it be made the capital of an expanded autonomous region.
"I will do my best to strengthen national
unity and brotherhood between Kurds
Iraqi Kurdistan President
Now, Barzani said, speaking first in Arabic and then in Kurdish, all must focus on the task of building "a unified, pluralistic, democratic, federal Iraq", in particular drafting a new constitution by 15 August.
"The constitution will decide the fate of all the people and thus should be a modern constitution reached by accord among all to guarantee a free and prosperous life for the citizens of Iraq."