An eerie emptiness enveloped the sacred Ka'ba in the Makkah Grand Mosque, Islam's holiest site, where attendance at Friday prayers was hit by measures to protect against the deadly new coronavirus.

An imam said during his sermon hoped for an end to the epidemic and backed a decision by Saudi Arabia's government to halt the year-round umrah pilgrimage. 

"God, I seek refuge in you from the calamity and the epidemic," said Sheikh Abdullah Awad al-Juhani, without mentioning coronavirus by name. 

"The measures by the kingdom to suspend umrah to limit the spread of this epidemic are in line with texts of the Sharia," he told worshippers.

While thousands of people attended the sermon, Friday prayers usually attract hundreds of thousands of worshippers.

"I had a very strange and difficult feeling as I was headed to the mosque," an Egyptian worshipper, who has lived in Makkah for six years but did not want to give his name, told AFP. 

"I felt deprived of the Ka'ba," he said, referring to the cube structure that is the focal point of Islam and draped in a gold-embroidered black cloth.

"The fact that it is empty (around the Ka'ba) is very scary," the 38-year-old engineer said.

The white tiles surrounding this focal point, at the heart of the Grand Mosque and around which Muslims circle in pilgrimage, were untrodden on Friday.

Authorities had emptied the Grand Mosque for sterilisation on Thursday, after announcing the halt to the umrah.

Friday "prayers took place inside the mosque and on the upper floors but not in the tawaf area" where people circle the Ka'ba, a mosque authority told AFP. 

Nearly half of the mosque's area was closed, he added. 

The area around the Ka'ba will remain closed for the duration of the umrah suspension as a "precautionary measure", but prayers inside the mosque will continue, the state-run Saudi Press Agency (SPA) reported.

Additionally, both the Grand Mosque and the Prophet's Mosque in the Muslim holy city of Madinah will be closed an hour after the evening "Isha" prayer to allow cleaning and sterilisation, it added.

The mosques will reopen an hour before the dawn "Fajr" prayer.