"Israel's step back from the metal detector implementation that offends Muslims is a step in the right direction, but it is not enough," Erdoğan said in a speech at Ankara's Higher Education Conference.
"Israel, benefiting from the weakness of Muslims, carries out illegal practices in Jerusalem, we won't be silent on Al-Aqsa," he added.
The Turkish president further warned that Israel is seeking to change the Islamic and historical character of Jerusalem, asserting the defense of Jerusalem was the responsibility of every Muslim.
He lamented that "Those who criticize our country whenever possible suddenly become silent when the issue is Palestine, Jerusalem, or Muslims’ rights or laws."
"Israel should honor the established customs of Jerusalem with respect to (international) law and human rights," Erdoğan continued. Al-Aqsa's door, he said, "cannot be closed to the Muslims of the world."
Erdoğan made similar accusations on Tuesday, telling legislators in the Turkish parliament that Israel "is using the fight against terrorism as a pretext to take al-Aqsa Mosque from the hands of Muslims."
"Everyone who knows Israel is aware that restrictions on Al-Aqsa mosque are not due to safety concerns," Erdogan said in what is considered to be his strongest statement on the Temple Mount crisis since it began.
Israel's Foreign Ministry called Erdogan's remarks "absurd, unfounded and distorted."
"The days of the Ottoman Empire have passed," it continued. "Jerusalem was, is, and will always be the capital of the Jewish people. In stark contrast to the past, the government in Jerusalem is committed to security, liberty, freedom of worship and respect for the rights of all minorities."
"Those who live in glass palaces should be wary of casting stones," the statement concluded.
Prime Minister Benjamin Netanyahu's office sarcastically wondered "what Erdogan would say to the residents of northern Cyprus or to the Kurds," saying that the Turkish president "is the last one who can preach to Israel."
The Turkish Foreign Ministry on Wednesday condemned the Israeli Foreign Ministry's response. Spokesperson Hüseyin Müftüoğlu described the statement by his Israeli counterpart Emmanuel Nachshon as "presumptuous" and called on Israel to fulfill its responsibilities by "acting with good sense, restoring the status quo (at the holy site) and lifting all hurdles to the freedom of worship."
"It is obvious that trying to cover up the fact that east Jerusalem has been under occupation will not benefit solving the Palestinian-Israeli conflict and achieving peace and stability in the region as the ongoing Israeli occupation has reached its 50th year in East Jerusalem, West Bank and Gaza," Müftüoğlu said.
Israel had installed metal detectors outside the Jerusalem shrine, holy to both Muslims and Jews, in response to an Israeli Arab shooting attack there that killed two police officers.
Palestinians claim Israel is trying to cement control over the site. Israel emphatically denies the claims insisting the security measures are in order to prevent further attacks.