Australians planning to travel to Saudi Arabia for the annual Hajj pilgrimage are being warned about a respiratory virus that has killed 46 people in the region.

Thousands of Australians are among the three million travellers expected to head to Mecca in October.

A total of 96 people have been infected with Middle East respiratory syndrome coronavirus across Saudi Arabia and neighbouring countries.

Dr Vicky Sheppeard from New South Wales Health says travellers need to be careful not to spread the virus.

"When it has gone there it has spread to other people, not widely but within hospitals and health care contacts," she said.

"As we will have Australians travelling to the Hajj, if they did catch the infection and bring it back here, it's important they're aware of that when they return and take precautions not to be spreading infection."