In a written statement, the ministry said more than thousand people were taken hostages in Azerbaijan's Upper Karabakh region.
"The fate of the missing people is still unknown today. This inhuman aggression against civilians was engraved in the memories of the international community and deeply wounded the common conscience," it said.
"Turkey commiserates deeply with her Azerbaijani brothers and sisters over this brutal attack and massacre which they suffered 26 years ago and shares their pain. We strongly condemn this massacre and the continuous occupation of the Azerbaijani territories by Armenia," the ministry added.
"We wish God’s mercy upon those who lost their lives in this massacre and wish once again our most sincere condolences to our Azerbaijani brothers and sisters."
The Khojaly Massacre is regarded as one of the bloodiest and most controversial incidents of the war between Armenia and Azerbaijan for control of the now-occupied Upper Karabakh region.
On the heels of the Soviet Union's dissolution, Armenian forces took over the town of Khojaly in Karabakh on Feb. 26, 1992, after battering it with heavy artillery and tanks, assisted by an infantry regiment.
When the massacre happened, the population of the town was more than 11,000.
The two-hour offensive also critically injured 487 others, according to Azerbaijani figures.