No reasons were given for the dismissal of deputy minister Ziad Memish.
The then health minister Abdullah al-Rabiah was dismissed in April without official explanation and replaced by labour minister Adel Fakieh, who 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.
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.
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Memish's dismissal comes as the health ministry said in its latest bulletin yesterday that 190 people have died of MERS in the kingdom, the country worst-hit by the virus which first appeared in September 2012.
It said the total number of infections was now 575.