Israel installed metal detectors at entrances to the Haram al-Sharif mosque compound, known to Jews as the Temple Mount, after an attack on July 14 that killed two policemen.
But after protests and intensive international diplomacy to prevent further unrest, the government removed the detectors from the site.
"Israel took the right step to remove the metal detectors to help lower tension," Erdogan said.
Jordan mourners chant 'death to Israel' after embassy shooting
"But is it enough according to our wishes? No, it is not," he said at a meeting on further education in the Islamic world in Ankara.
Erdogan said Turkey "cannot tolerate" constraints placed on Muslims visiting the site during Friday prayers.
Palestinians viewed the new security measures as Israel asserting further control over the site, which is central to the Israeli-Palestinian conflict.
Clashes broke out during protests, leaving five Palestinians dead.
"The Israeli government want to destroy the Islamic character of Jerusalem with a new practice every day," Erdogan said.
Palestinians die in new clashes over Jerusalem holy site
There were tit-for-tat statements from both sides after Erdogan criticised Israel on Tuesday and accused it of "attempting to take the (Al-Aqsa) mosque from Muslim hands".
The Israeli foreign ministry said in a statement that his comments were "mind-blowing, false and distorted".
Turkish foreign ministry spokesperson Huseyin Muftuoglu on Wednesday condemned Israel's "arrogant" remarks.
COMMENTS (1)
Comments are moderated and generally will be posted if they are on-topic and not abusive.
For more information, please see our Comments FAQ