As regards the bilateral ties between Iran and Turkey, President Rouhani said the two governments are resolved to raise the value of annual trade exchange to $30 billion.
"We want security and stability in the Middle East. the independence referendum in Iraq's Kurdistan is a sectarian plot by foreign countries and is rejected by Tehran and Ankara".
"Iran and Turkey should take every possible measure against the move and the Iraqi government, too, should make decisions and take serious action", Khamenei added.
Mr Erdogan said Ankara was considering taking further measures against Iraqi Kurdistan.
In addition to northern Iraq, the crisis in Syria is expected to be discussed.
Those exercises have also involved forces of the federal government in Baghdad, which has demanded the annulment of the September 25 vote, which returned a 92.7 percent majority for independence.
It may be mentioned that amid shared fears, Mr. Erdogan and Mr. Rouhani united against Kurdish independence.
Turkish President Recep Tayyip Erdogan arrived in the Iranian capital on Wednesday for key talks with senior Iranian officials. Both expressed their willingness to work together and with the government of Baghdad, which deemed the vote "illegal". He also said that his country never harmed Kurdish population.
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In the same time-frame, the amount imported from Iraq dropped by 20%, as Iran replaces Iraq as the top supplier to Turkey.
Israel has denied Turkey's previous claims of involvement in the vote, but has welcomed the Kurds' vote for independence.
According to him, the creation of a new state in Iraq is risky both for Turkey and Iran.
Baghdad already has imposed sanctions on Kurdish banks and halted foreign currency transfers to the region, and a flight ban has halted all global flights from servicing the Iraqi Kurdish territory's airports.
Turkey has threatened to close its land border and halt the export of oil from Iraqi Kurdistan to the Turkish port of Ceyhan, an economic lifeline.
Erdoğan said the referendum had no legitimacy and had only been recognized by Israeli regime.
Erdogan is also due to meet Iranian Supreme Leader Ayatollah Ali Khamenei on his one-day official trip to Iran.
Emphasising joint fight in Syria against ISIL and al-Nusra Front, Erdoğan said: "I am sure that as the result of this fight, we will help the oppressed Syrian people and common efforts to defend all the oppressed people of the world is our duty".