"A total of 140 cases of measles have been reported in the province," the ministry said in a Monday statement.
It said four of the six victims had died in their homes, while the remaining two had passed away in hospital.
The Health Ministry added that the condition of 110 other measles patients had already improved, while 24 others were still receiving treatment.
Within the past three months, around 1,356 Egyptians have contracted the disease, according to the ministry, which has not disclosed where the cases had been recorded.
Health Minister Adel Adawi on Monday paid a visit to Egypt's northeastern Siwa Oasis, an administrative division of Marsa Matrouh, where large numbers of measles infections have been reported.
He said the ministry had already sent 70,000 anti-measles vaccines to the oasis town.
The Health Ministry had earlier sent convoys of medical specialists to Marsa Matrouh as part of a government initiative aimed at fighting the disease.
Measles is an airborne disease, symptoms of which usually develop between seven and 14 days after exposure to an infected person.
Initial symptoms include high fever, spots in the mouth, malaise and appetite loss.