Observers, including the Organisation for the Prohibition of Chemical Weapons (OPCW), have previously accused IS of using mustard gas in Syria and described the possibility as extremely worrying.
"After a rocket was fired by Daesh (IS), 22 opposition members were observed to have been exposed in their eyes and bodies to chemical gas," the general staff said in a statement, quoted by the state-run Anadolu news agency.
It said the attack happened in the area of the village of Khaliliya, east of Al Rai in northern Syria, where the pro-Ankara fighters backed by Turkish special forces and air power are battling to dislodge the jihadists from the border area.
The report did not specify what type of gas was used.
Turkish media said the affected Syrian fighters were brought over the frontier to the Turkish border town of Kilis by teams from Turkey's AFAD emergencies agency.
The reports said the Turkish emergency workers were equipped with special chemical suits to protect themselves. The Syrians were brought to the main hospital in Kilis where they are undergoing treatment.
Television pictures showed some of the Syrians being transferred on stretchers to the hospital, with the emergency workers dressed in full-body white protective clothing and gas masks.
The incident comes amid growing fears over the use of chemical weapons on Syria's over five year civil war.
A joint UN and OPCW backed panel established during a year-long investigation that forces of Syrian President Bashar al-Assad carried out three chlorine gas attacks on villages in 2014 and 2015.
But the panel, known as the Joint Investigative Mechanism (JIM), also found that the Islamic State group in Syria used mustard gas as a weapon in August 2015.
Earlier this month, the UN Security Council unanimously decided to extend for another year the panel's mandate.
OPCW director general Ahmet Uzumcu told AFP earlier this month that IS may have itself manufactured mustard gas used in attacks in Syria and Iraq.
He said analysis of samples of mustard gas used was was "poor quality, but still harmful ... and it was weaponised so it's extremely worrying".
The Turkish army is backing the Syrian fighters in an unprecedented incursion aimed at rooting out IS jihadists from the border area and also ensuring there is no Kurdish militia presence.
In a three-month operation, the rebels have so far captured the IS stronghold of Jarabulus, cleared IS from Al Rai and retaken the symbolically important town of Dabiq without much resistance.
With Turkish support they are now pressing to take Al Bab, another town deeper inside Syria, from the jihadists in an advance that appears to be taking more time and encountering greater opposition.
Tensions are running high after six Turkish soldiers were killed in the last week alone, two by IS but four in an air strike it believed was carried out by forces of Assad.
On Saturday, Turkish President Recep Tayyip Erdogan and President Vladimir Putin of Russia, Assad's main ally, discussed the Syria conflict by telephone for the second time in just over 24 hours, both sides said.
The Turkish armed forces said that four IS targets had been destroyed in the latest air raids by Turkish war planes over northern Syria.