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More than 200 people were wounded when Israeli riot police stormed the Al-Aqsa mosque compound late on Friday, firing tear gas and rubber-coated bullets at thousands of worshippers gathered in the last days of the Muslim holy month of Ramadan.
"This development of events is perceived with deep concern in Moscow. We strongly condemn attacks against civilians," the foreign ministry said in a statement.
"We call on all parties to refrain from any steps fraught with the escalation of violence."
The clashes came as tensions have soared over Israeli restrictions on access to parts of the Old City during Ramadan and the threat of eviction hanging over four Palestinian families in occupued east Jerusalem to make way for Israeli settlers.
In its statement, Russia's foreign ministry said it reaffirmed Moscow's position that "the expropriation of land and property located on it, as well as the creation of settlements by Israel in the occupied Palestinian territories, including East Jerusalem, have no legal force".
"Such actions are a violation of international law and impede the achievement of a peaceful settlement based on the creation of two states - Palestine and Israel."
Israel occupied east Jerusalem, along with the West Bank, during the 1967 Arab-Israeli war.
Authorities later annexed east Jerusalem in a move considered illegal under international law. Israel views Jerusalm as its undivided capital, while Palestinians seek to claim east Jerusalem as the capital of a future state.
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