"We condemn Israel and the Trump administration for causing the developments happening today at the al-Aqsa Mosque and West Bank," Bekir Bozdag said on his Twitter account.
"The U.S. administration is the first-degree offender for all kinds of crises, chaos, and conflict that will happen today and afterwards,” he added.
"U.S. President [Donald] Trump's decision to move the U.S. Embassy in Tel Aviv to Jerusalem has ended the ongoing fragile peace process," he added.
On Israeli troops using ammunition and tear gas to disperse Palestinian protesters, Bozdag called on Israel to use "common sense" and to "end the violence".
Thousands of Palestinians staged rallies across the West Bank and East Jerusalem after Friday prayers to protest Trump’s decision, which was announced Wednesday.
The dramatic shift in the U.S. policy sparked demonstrations on Thursday in the occupied Palestinian territories as well as Turkey, Egypt, Jordan, Tunisia, Algeria, Iraq and in some other Muslim countries.
Jerusalem remains at the heart of the Israel-Palestine conflict, with Palestinians hoping that East Jerusalem -- now occupied by Israel -- might eventually serve as the capital of a future Palestinian state.