This "neo-sectarian" approach aims to rally Syrian Shiites to Assad's side and explain away opposition to him by majority Sunni states in the region, Ibrahim Kalın told Reuters.
But Syria's Sunnis and Alawite sect, an offshoot of Shiism to which Assad belongs, are not fixed blocs and Turkey does not see the crisis in sectarian terms, Kalın said at a weekend conference of Muslim and Christian religious leaders from the Middle East.
"The Assad regime, because it has lost its political legitimacy, is now trying to present this as a sectarian conflict," he said. "They claim that those who oppose the Assad regime do so because they are Sunnis and they hate Shiites.
"The good news is that the vast majority of the Sunnis and Shiites don't buy this argument and realize these are political decisions, not a sectarian conflict."
Kalın described as "neo-sectarianism" the growing emphasis on religious identities across the Middle East, but said these trends -- while real -- were still mostly secondary to the political struggles driving events in the region.
Syrian society is a religious and ethnic mosaic with multiple fault lines. The Alawites who comprise the bulk of the ruling establishment make up 12 percent of the population, while Sunnis, the backbone of the opposition, account for 75 percent.
There are also Christian (10 percent), Kurdish (8 percent) and Druze (less than 3 percent) minorities. Christians have stayed mostly neutral in the fighting, fearing an Islamist victory if Assad goes. Syrian Kurds have used Assad's weakness to take control of some northern areas of the country.
More about Israel than Islam
In Ankara's analysis, Shiite Iran's staunch support for Assad is partly due to sectarian solidarity, but is based more on flawed political assumptions.
"Iran considers Syria to be a sphere of influence and part of a front against Israeli occupation in the region," Kalın said.
"Their calculation is that, if the Assad regime is toppled, the new regime in Syria would not hold its ground against Israeli policies, which is simply wrong."
The newly elected governments in Tunisia, Egypt and Libya have proven very concerned about the Palestinian cause, and they now express their opposition to Israeli occupation of Arab land with full democratic credentials, he said.
"Whoever comes to power in Syria will be based on the popular will of the people. The vast majority of the Syrian people, just like the rest of the Middle East, are against the Israeli occupation," he added.
Kalın, a former professor of Islamic philosophy and leading advocate of better Muslim-Christian understanding, said Islam's majority Sunnis and minority Shiites have had phases of both calm and tense relations throughout Islam's history.
They also have splits within their own ranks and varied experiences of living together in different countries.
"Both historically and doctrinally, it would be a big mistake to treat the Sunnis as one bloc and the Shiites as one bloc," he argued. "There's no one single indicator that can really define that whole identity."
Salafis hit both Sunnis and Shiites
Kalın said Saudi Arabia and Qatar, which have backed conservative Sunni movements in other recent uprisings in the Arab world, also put politics before religion in Syria.
"They are supporting the Syrian opposition against a brutal regime -- that's the bottom line there," he said.
Erdoğan, a Sunni, impressed the meeting of religious leaders in İstanbul by using an iconic Shiite image -- the killing of Imam Hussain, a grandson of the Prophet Mohammad, in a battle in 680 in Kerbala in Iraq -- to denounce the bloodshed in Syria.
"What is happening today in Syria is the same as what happened in Kerbala 1,332 years ago," he said on Friday, comparing the Syrian people to the slain Shiite Hussain and Assad to the rejected Sunni leader who killed him.
"This is not a Sunni or Shiite issue, it's a matter of justice and oppression," Kalın said.
Neo-sectarianism is also evident in the radical Salafi ideology that rejects both Shiites and other Sunnis as heretics who have strayed from the purity of early Islam, he said, noting that Salafis had recently destroyed several Sufi Muslim shrines in Libya.