Syrian's government and allied forces backed by Russia and Iran have swiftly recaptured other rebel strongholds in the southwest and vowed to push on and recover all of the country.
Speaking to reporters in Ankara before heading for a summit of emerging market countries in South Africa, Erdogan described the situation in Daraa and Idlib—where Turkey has set up a dozen military observation posts—as troublesome.
"We will be discussing Daraa (with Russia), which is one of the most problematic issues of all. There is also the issue of Idlib, which we will discuss because in these places anything can happen at any time," he said.
"What we want is that Syrian people would be protected from these attacks and particularly the brutal attacks of some organisations in the region," Erdogan said.
Forces loyal to Syrian President Bashar Assad, backed by the Russian military, have captured most of the southern province of Daraa in an offensive that began in June.
Daraa city was the scene of the first major peaceful protests against Assad in March 2011 which spiralled into a war now estimated to have killed half a million people.
Erdogan has already raised the issue of Idlib with Putin in a telephone conversation in mid-July, saying an attack by the Syrian army
Erdogan said the avoidance of "negative developments" in Idlib was important in terms of encouraging rebel groups to attend a meeting in Astana planned for July 30-31, according to a source at the Turkish presidency.
Referring to Turkey's relationship with Iran, Erdogan has argued against severing economic ties with Iran as the United States readies for sanctions.
Speaking in Ankara, President Erdogan said it goes against the independence of states to cut ties with its "neighbor and strategic partner" because the US demands it.
President Donald Trump announced in May that he would pull out of a 2015 agreement over Iran's nuclear program and would re-impose sanctions. His administration threatened countries with sanctions if they don't cut off Iranian oil imports by early November.
Turkey imported 3 million tons of crude oil from Iran in the first four months of 2018, amounting to 55 percent of crude supplies and 27 percent of its total energy imports.
Erdogan asked Wednesday: "Who will heat my country throughout the winter?"