"A comprehensive revision" going back to 2012 has resulted in revising up the death toll, which had stood at 190 people, while the number of infected cases rose from 575 to 688 people, the ministry said in a statement.
Earlier Tuesday, the health ministry announced that acting minister Adel Fakieh had sacked one of his deputies, Ziad Memish, without giving reasons for the dismissal.
Fakieh, who is the labour minister, was assigned the health portfolio after former health minister Abdullah al-Rabiah was himself dismissed in April without official explanation.
Upon his appointment, Fakieh promised "transparency" in providing the public and media with information about the Middle East Respiratory Syndrome.
MERS is considered a deadlier but less transmissible cousin of the SARS virus that appeared in Asia in 2003 and infected 8,273 people, nine percent of whom died.
Like SARS, it appears to cause a lung infection, with patients suffering coughing, breathing difficulties and a temperature. But MERS differs in that it causes rapid kidney failure.
Last month, Fakieh announced he was sacking the head of the King Fahd Hospital in the western city of Jeddah, where a rise in MERS infections among medical staff sparked panic among the public.
Most cases of the disease have been in Saudi Arabia, but the virus has been imported to more than a dozen other countries.
All of those cases relate to people who became ill while in the Middle East, with some involving pilgrims travelling to Muslim holy sites in Saudi Arabia.