President Recep Tayyip Erdoğan arrived in Tehran with a high-level delegation Wednesday on an invitation from Iranian President Hassan Rouhani.
Israel has been among the only countries to openly support an independent Kurdish state, and many Kurds have openly welcomed Israel's support, drawing accusations from Arab leaders that last week's referendum was a Zionist plot.
Iranian Supreme Leader Ayatollah Ali Khamenei has described the recent referendum on independence held in northern Iraq as "treason" against the region.
Both the Iranian and Turkish militaries launched exercises near the border just before the KRG independence referendum.
"What is the objective of the referendum in Northern Iraq Regional Administration?"
He said Ankara and Tehran would not recognise the referendum.
Over the past year, Turkey's oil imports accounted for 96.6 percent of Iraq (9.2 million tons), Iran (6.9 million), Russian Federation (3.2 million), Kuwait (2.5 million) and Saudi Arabia (2.1 million).
Mr Rouhani also said that Tehran and Ankara are planning to expand their economic ties.
For his part, Rouhani underlined the importance of co-operation between Turkey and Iran to "combat terrorism" in the region.
Iraq's central government also opposes the vote.
Officials and analysts fear the vote could lead to further instability in the Middle East, a region already ravaged with wars in places like Syria and Yemen. "Turkey, Iran, and Iraq have no choice but to take serious and necessary measures to protect their strategic goals in the region".
He added that the two countries will continue their fight against terror groups, such as Daesh, Jabhat Fateh al Sham and the PKK.
He also referred to the need to promote the level of political, trade, economic, cultural and tourism relations between the two countries, saying: "Development of all-inclusive relations with Iran is in the interests of the two nations".
He continued: "We also discussed a tripartite mechanism for Syria, and Iran, Russia and Turkey have started the process of negotiations in Astana, and we have taken steps within that framework".