Turkey is already hosting at least 1.5 million refugees displaced by the Syrian conflict and has repeatedly warned that its capacities are being strained by the numbers.
Cavusoglu said supporting the rebel Free Syrian Army (FSA) was the only option for the international community against what Ankara sees as the twin threat of Islamic State jihadists and the regime of President Bashar al-Assad.
"The main force fighting both ISIS and the Syrian regime today is the Free Syrian Army," he said, using another term for the Islamic State group.
"But it has failed to achieve the desired outcome because it is fighting against both groups," he told reporters in Ankara alongside his Finnish counterpart.
'LOSS OF HOPE FOR SYRIA'
Cavusoglu said there was little difference between IS militants and the Assad regime.
"Both of them are killing people brutally and don't refrain from using any kinds of weapons at their disposal. Both force people to flee their land."
He added: "An advance on Aleppo would mean an influx of two to three million people to the Turkish border."
He said a weakening of the moderate opposition to Assad and the FSA would "result in the advance of the unstoppable ISIS as well as the regime".
"And this will make Syria even more unstable. Therefore, the advance of both of them should be halted."
Turkey has repeatedly called for the ousting of Assad as the sole way to resolve the Syrian crisis permanently.
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But it has grown increasingly concerned in recent months that the US-led coalition strikes against IS could end up strengthening the Assad regime.
Ankara has been seeking to persuade the United States a three-pronged approach is needed to strike against IS, Assad and Kurdish militants. But it is unclear if its arguments have made any headway with Washington.
Turkey is pressing for a no-fly zone and a security zone to be imposed inside Syria along its 911 kilometre (566 mile) border with the country to ensure its security.
A senior aide to President Recep Tayyip Erdogan said Tuesday that there was an "unholy alliance" between IS and Assad in the battle for Aleppo that had to be broken by the FSA.
"If Aleppo is allowed to fall, it would be the loss of any hope for the future of humanity in Syria," Ibrahim Kalin wrote in the Daily Sabah newspaper.
In recent months, Assad's forces have advanced around the outskirts of the eastern portion of Aleppo that is under rebel control, threatening to encircle it completely.
Rebel-held areas of Aleppo are under the control of multiple groups, including fighters affiliated with the FSA.
Meanwhile the Turkish online newspaper Radikal reported that the chief of the moderate anti-Assad group the Syrian Revolutionary Front, Jamal Maarouf, had fled to Turkey two weeks ago.
There was no confirmation of the report and no further details were immediately available.
Media reports said at the weekend that Turkey and the United States have agreed a plan under which some 2,000 FSA fighters would be trained on Turkish soil.