A two-year-old child died in Jeddah and a 53-year-old man died in Eastern Province, where the outbreak has been concentrated, the ministry said late on Saturday in a statement on its website. Four people have died outside the kingdom.
The ministry said another three people had been confirmed as being infected with Middle East respiratory syndrome (MERS), bringing the total number of confirmed cases inside the kingdom to 65 since it was identified a year ago.
On Friday the World Health Organisation said MERS, which can cause fever, coughing and pneumonia, had not yet reached pandemic potential and may simply die out.
Ramadan, Islam's fasting month, is expected to start in Saudi Arabia on Monday night and is traditionally a time when hundreds of thousands of Muslims come to Mecca for umrah, a pilgrimage that can be carried out at any time of year.
Millions are also expected to travel to Mecca for the main pilgrimage, haj, that will take place in October, although the authorities have cut the number of visas this year, citing safety concerns over expansion work at the main mosque site.
WHO experts said last month that countries at risk from MERS should put in place plans for handling mass gatherings but has stopped short of recommending restrictions on travel.