Erdogan, who is increasingly touting himself as a leader of the Muslim world, said he would take steps to calm the tensions by meeting Islamic leaders.
The Turkish president, a devout Sunni Muslim, made the comments in a closed briefing to Turkish reporters while returning on his visit to Shiite Iran earlier this week.
"At this moment the Islamic world is facing the risk of disintegration," Erdogan was quoted as saying by Turkish dailies including Hurriyet and Sabah.
"Steps need to be taken quickly to thwart these attempts" to cause the disintegration, he added.
"You can have a different denomination (of Islam) but if you seek to impose one denomination on another you will break up the ummah (Islamic community)," he said.
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Erdogan said international organisations including the Organisation of Islamic Cooperation (OIC) should show they are sincere about halting the violence in flashpoints like Iraq, Egypt, Libya, Syria and Yemen.
But Erdogan said he would also play a role and revealed he was planning visits to Asian Muslim powers Indonesia and Malaysia and would also once again visit Saudi Arabia.
He said all the regional crises, including Yemen, were on the agenda when he held talks on Tuesday with Iranian President Hassan Rouhani and supreme leader Ali Khamenei.
"The groups in Yemen should meet and work on possible solution. Saudi Arabia, Turkey and Iran should be involved in efforts for a diplomatic solution," he said.
Turkey has strongly backed the military action by fellow Sunni Muslim power Saudi Arabia against Iran-allied Huthi rebels in Yemen, to the anger of Iran.
Erdogan said proposals agreed during a meeting on Monday with Saudi deputy crown prince and Interior Minister Mohammed bin Nayef had been conveyed to Iran during his visit.
Turkey during Erdogan's rule, first as premier and now as president, sought to place itself as the centre of the Islamic world, although some commentators argue its moved backfired and simply created more enemies.