Turkish President Recep Tayyip Erdogan called Syrian President Bashar al-Assad a "murderer" on Wednesday.
"Autopsies were carried out on three of the bodies after they were brought from Idlib. The results of the autopsy confirms that chemical weapons were used," Justice Minister Bekir Bozdag said, quoted by state-run Anadolu news agency.
"This scientific investigation also confirms that Assad used chemical weapons," Bozdag added, without giving further details.
Thirty-two injured Syrians were brought to southern Turkey for medical treatment but three of them died in hospital.
At least 86 people were killed early on Tuesday in Khan Sheikhun and dozens more were being treated after they were found convulsing and foaming at the mouth.
Autopsies were conducted by officials from the World Health Organization in the southern province of Adana together with officials from Organisation for the Prohibition of Chemical Weapons, Bozdag said.
The wounded had been brought from Idlib through Turkey's Cilvegozu border gate for the treatment in the Reyhanli district of Hatay province.
Turkish President Recep Tayyip Erdogan, a vocal critic of Assad, called the Syrian president a "murderer" on Wednesday after denouncing the world's "silence" on the deaths.
Russia, Assad's main ally, has said a Syrian air strike had hit a "terrorist warehouse" but Erdogan has yet to make any reference to the Russian claim.
Moscow has been one of the regime's biggest supporters together with Iran while Turkey has given support to Syrian opposition fighters.
Recently Ankara said it "successfully completed" its military operation supporting Syrian rebels against the Islamic State group launched last August in northern Syria.