The council statement was issued late Thursday after three days of clashes at the hilltop compound known to Muslims as the Noble Sanctuary and to Jews as the Temple Mount.
Rumors had spread among Palestinians that Jewish "settlers" were plotting to take over the site. Police entered the compound to disperse Muslim protesters who had holed up in the mosque and hurled rocks, concrete blocks and firebombs at security forces.
The council statement says Muslims at the site "must be allowed to worship in peace, free from violence, threats and provocations."
It also says that "visitors should be without fear of violence or intimidation."