"We do not accept and strongly condemn Israeli violence against Palestinian worshippers at Al-Aqsa Mosque compound," ruling Justice and Development Party (AK Party) Spokesperson Ömer Çelik said in a statement late Monday.
In a later speech, President Recep Tayyip Erdoğan also condemned the raid.
"What's happening in Al-Aqsa is a great sadness for us," he said.
"We discussed such matters with Israeli President Isaac Herzog when he was in Ankara; we hope that such actions won't be repeated in the future," he added in a speech during an iftar dinner with ambassadors in Turkey.
Hundreds of Jewish settlers stormed into the Al-Aqsa Mosque compound in occupied East Jerusalem, a Palestinian agency reported earlier.
Nearly 560 settlers stormed the flashpoint site under heavy police protection, the Islamic Endowment Department that oversees the mosque compound said in a statement.
The settlers toured the complex for about three and a half hours before leaving the site, the statement added.
Ahead of the settler incursion, Israeli police forced Muslim worshipers to evacuate the mosque’s courtyards, according to eyewitnesses.
Tension has mounted across the Palestinian territories since Israeli forces raided the Al-Aqsa Mosque courtyard on Friday amid clashes with worshippers, injuring hundreds. On Sunday, more than 700 Israeli settlers forced their way into the complex to celebrate the weeklong Jewish Passover holiday.
Al-Aqsa Mosque is the world's third-holiest site for Muslims. Jews call the area "Temple Mount," claiming it was the site of two Jewish temples in ancient times.
