In an urgent circular to doctors, it said the Saudi health ministry "has taken the decision to restrict the issuing of visas" for the annual hajj and for the umrah, a pilgrimage which can be undertaken at any time.
"Elderly persons (for whom no precise age threshold has been specified), pregnant women, children and people affected by chronic diseases, notably people with cardiac, diabetic or respiratory disease, kidney or immune-system deficiencies, will be unable to obtain a visa this year," the circular said.
The circular was issued by the General Health Directorate (DGS), which administers the health ministry.
In a statement posted on its website on Saturday, the Saudi health ministry urged people in these categories not to perform the hajj.
But the statement was unclear as to whether the authorities would not issue these people with a visa.
Middle East Respiratory Syndrome (MERS) has caused 45 deaths, 38 of them in Saudi Arabia, according to the World Health Organisation (WHO), which convened emergency talks on the virus last week.
The WHO has not recommended any MERS-related travel restrictions, but says countries should monitor unusual respiratory infection patterns.
A cousin of Severe Acute Respiratory Syndrome (SARS) in the coronavirus family, MERS infects lungs, causing fever, coughing and breathing difficulties, and can also cause kidney failure.