Saudi Arabia says 1301 Muslim pilgrims died during the Hajj, the annual pilgrimage to Mecca, primarily due to a heatwave that saw temperatures hit nearly 52C.

Some 83 per cent of the fatalities were unregistered pilgrims, Saudi Health Minister Fahd al-Jalajel said.

The vast majority of these pilgrims did not participate with the official delegations from their respective countries.

“The unregistered pilgrims walked for long distances under the sun without a shelter and rest. A number of them were elderly and some others had chronic diseases,” al-Jalajel told the Saudi state television al-Ekhbariya.

In its statement, the government said16 travel agencies failed to provide adequate services for pilgrims.

The government said officials from the companies have been referred to the public prosecutor for investigations.

The health ministry said they contacted the families of the deceased, a complex task since many “did not carry any identification.”

“The necessary procedures have been carried out to identify them, bury them, and honour them in Mecca, and their death certificates have been issued,” it added.

Unregistered pilgrims usually have no access to accommodation and transportation services.

Health and security sources in Egypt put the number of Egyptian nationals who died at 672.

Indonesia was the second most affected country with around 200 deaths among pilgrims followed by India (98 deaths) and Jordan (75 deaths), all due to “extreme heat.”

Most of the countries that reported casualties during the pilgrimage do not specify the causes of death.

Countries have an official mission where participants have permits and visas issued exclusively by Saudi Arabia for the pilgrimage, but due to the high cost of this trip, averaging $US5000 ($7530) per person, many opt for other routes that Saudi Arabia considers illegal.

Some 1.8 million pilgrims took part in this year’s Hajj. One of the five pillars of Islam, the Hajj is a mandatory duty for all Muslims to complete once in a lifetime, if they have the financial and physical means to do so.