Jerusalem's Great Synagogue will be closed for the first time over the Jewish New Year due to the novel coronavirus, authorities said Wednesday, as Israelis braced for a second lockdown.

Israel has registered the world's highest coronavirus infection rate over the past two weeks, according to an AFP tally. It is set to be the first country to enforce a second nationwide shutdown.

The measures announced by Israeli Prime Minister Benjamin Netanyahu will come into force on Friday afternoon, hours before the start of the New Year festival known as Rosh Hashanah.

The three-week lockdown is set to remain in place over the Jewish holidays of Yom Kippur and Sukkot, a period when synagogues are usually filled with worshippers.

The Great Synagogue's board of directors announced the New Year closure in a statement posted on its website on Wednesday.

Israeli authorities have published guidelines to limit the number of worshippers based on the size of a building, meaning it could in theory welcome about 200 people.

"But we decided we won't take any risks," the Great Synagogue's president, Zalli Jaffe, told AFP.

The holy site usually welcomes between 1,100 and 1,700 worshippers for each service during the Jewish holidays.

"We have never closed since its creation," said Jaffe, 67, who has prayed at the site since childhood.

Built on the foundations of a much smaller synagogue, it was inaugurated in 1982. As the official place of worship for the Jewish state, the Israeli president traditionally attends on Yom Kippur.

The onset of the coronavirus pandemic prompted the Great Synagogue to close in March, and its doors have remained shut ever since.

Israel has registered nearly 167,000 coronavirus cases and 1,147 deaths, out of a population of nine million.

Under the new Israeli measures most places of worship will be allowed to welcome a maximum of 10 people at a time.

On Wednesday, the authority that administers Jerusalem's Muslim holy places announced the Al-Aqsa mosque compound would be closed for the duration of the lockdown.

Jordan is the custodian of the compound, known by Muslims as the Haram al-Sharif, or Holy Sanctuary, and as the Temple Mount by Jews.

It is only the second time that the Waqf authority has decided to close the compound since Israel occupied east Jerusalem in the Six-Day War of 1967.