"We will work on the prosperity of our capital Jerusalem and will pass many decisions related to the development of the city," Netanyahu said in a statement to reporters.
"Enemies have tried in the past to erase us from the map, and this is what Hamas, Hezbollah, and Iran are trying to do today," he added.
Today marks the "Jerusalem Day" – an official Israeli national holiday that marks the "Naksa" or the six-day war of 1967, which saw Israel occupy East Jerusalem and the West Bank.
Hundreds of Israelis, flanked by Israeli police, stormed the courtyards of al-Aqsa Mosque on Wednesday morning to participate in the annual Flag March of "Jerusalem Day".
The flag march is a flag-flying parade where tens of thousands wave "Israeli" flags while marching through Damascus Gate to the Western Wall.
Meanwhile, the Islamic Waqf Ministry in Jerusalem said that 928 settlers had stormed the al-Aqsa Mosque since Wednesday morning.
The settlers performed Jewish rituals and dances during their incursion into al-Aqsa, while the Israeli forces prevented the Palestinians from entering the mosque and only allowed the elderly.
The Israeli police deployed three thousand personnel to secure the settlers' safety through the march.