In a statement, the charity, also known as Medecins Sans Frontieres (MSF) said the geographic scale of the epidemic was unmatched.
MSF coordinator Mariano Lugli said: "We are facing an epidemic of a magnitude never before seen in terms of the distribution of cases in the country."
Mr Lugli said previous outbreaks handled by MSF were "much more geographically contained and involved more remote locations."
He added: "This geographical spread is worrisome because it will greatly complicate the tasks of the organisations working to control the epidemic."
Medics must wear sealed biohazard suits when caring for the victims Guinea's health ministry has reported 122 suspected cases, with at least 78 deaths linked to the virus. Of those there are 22 laboratory confirmed cases.
Some of the cases are in Guinea's capital Conakry. Liberia also confirmed its first cases overnight on Sunday.
One of two women who tested positive for the virus has died, while the other, her sister, has been isolated in a medical centre outside the capital Monrovia.
Sierra Leone is investigating five suspected cases, although none have yet been confirmed.
Macenta was one of the first towns in Guinea to report the virus It is not only the geographic scale which makes this outbreak more severe.
There are five recognised strains of Ebola - four of which are deadly to humans.
The Guinean government says the strain it is currently observing is the 'Zaire' strain - the most aggressive of the five. It kills roughly 90% of its victims.
There is no known treatment or vaccine.
Ben Neuman, a virologist with the University of Reading, told Sky News: "The real worry is that this virus has been found in Conakry.
"This is a city where the population density is getting close to 10,000 per square kilometre and setting one of these at least mildly contagious viruses loose in that kind of population centre really has the makings of a humanitarian disaster."
Aid workers are transporting tons of medical equipment to affected areas The outbreak has also spread panic among other countries in the region.
Senegal has closed its border with Guinea and suspended weekly markets near the border to prevent the virus travelling further.
Sierra Leone has introduced a screening process on its border with Guinea, while regional airline Gambia Bird has delayed the launch of services to Guinea's capital.
MSF has sent dozens of aid workers into Guinea in an attempt to prevent a further spread.
It said a total of 60 people, experienced in working on haemorrhagic fever, will be in the country by the end of the week.
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