"Their implementation is wrong. Taking such radical measures over a terror threat, blocking or restricting Muslims' access to Al-Aqsa Mosque, will not contribute to solving any problems," Yildirim was quoted as saying by Anadolu news agency.
According to Yildirim, such measures would only damage "tolerance" between different religious groups.
"I hope that in the near future everything will return to normal," the prime minister added.
On July 14, two Israeli police officers died and another one was wounded after three armed assailants opened fire at the Temple Mount complex. The police pursued and killed the assailants. Following the attack, the site was cleared of visitors and closed off to carry out searches.
The Temple Mount is under the autonomous administration of the Waqf and only the followers of Islam can pray on the site, while representatives of other religious traditions are allowed to visit it freely.