"We have a common stance (with Russia) over the DAISH terrorist organisation there," Turkish President Recep Tayyip Erdogan told a joint news conference with his Russian counterpart, Vladimir Putin, referring to IS by its Arabic acronym.
"There has been no problem over the issue of terrorism. We occasionally see how much Russia has suffered from terrorism and we know that there cannot be an understanding such as 'your terrorist' and 'my terrorist'," he added.
Putin similarly said: "We do not want chaos in Syria, nor the strengthening of terror groups."
Turkey had vehemently denied claims it backed IS, which has taken swathes of Iraq and Syria right up to the Turkish border.
Erdogan's comments came a day after Pope Francis said that he had told the president in a meeting last week that "it would be wonderful if all the Muslim leaders of the world... spoke up clearly and condemned" terror carried out in the name of Islam.
Turkey and Russia stand on opposing sides over the crisis in neighbouring Syria, with Ankara being one of the fiercest critics of President Bashar al-Assad.
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But Moscow remains one of Assad's few allies, routinely blocking resolutions against his regime in the UN Security Council.
"We have agreed with Mr President that a solution is needed (on Syria) but the problem is how," said Erdogan. "It is impossible to reach a solution with Assad."
Putin said the question should be answered by the Syrian people, adding that Assad received overwhelming support in the June presidential elections.
"But we don't think the situation is normal there and we are working for a satisfying result in consultation with all the actors involved."
But Erdogan was swift to denounce the notion that Assad had popular legitimacy.
"Coup rulers come to power in the world by taking a high percentage of votes... There is an attempt to legitimise a person who came to power (in Syria) through anti-democratic means," he said.