The two men, aged 78 and 55, had also suffered from other chronic diseases, the ministry said on its website. It did not specify when the deaths occurred.
Meanwhile, authorities recorded two more infections bringing to 119, the number of people infected in the kingdom since the disease first appeared in Saudi Arabia in September 2012, the ministry said.
The MERS virus has so far claimed 58 lives worldwide, with the greatest number of deaths from the respiratory disease -- 51 -- in Saudi Arabia itself, including the latest two.
"So far, no case of any epidemic has been recorded among the pilgrims, especially the coronavirus," Rabia said.
Also Read
The hajj is one of the largest gatherings in the world, and there are fears that pilgrims, expected to reach two million this year, could be infected and return to their homelands carrying the virus.
The hajj takes place in the holy city of Mecca, located about 800 kilometres west of Riyadh.
Riyadh has, however, urged the elderly and chronically ill to avoid the hajj. Authorities have also advised pilgrims to wear face masks.
Experts are struggling to understand MERS, for which there is no vaccine.
It is considered a deadlier but less-transmissible cousin of the SARS virus that erupted in Asia in 2003 and infected 8,273 people, nine percent of whom died, and sowed economic chaos.