"It is deteriorating faster, and moving faster, than we can respond to," Joanne Liu told reporters a day after returning from a 10-day mission to the hard-hit region.
"It is like war time. There is fear," she said.
"It's moving, and advancing, but we have no clue how it's going. Like in a war time, we have a total collapse of infrastructure," she added.
The outbreak started at the beginning of this year in the forested border zone between Guinea, Sierra Leone and Liberia, and has also spread to Nigeria.
While Guinea had initially been the hotbed, the pace of the outbreak there has slowed, with concerns now focused on the other countries, notably Liberia.
"If we don't stabilise Liberia, we'll never stabilise the region," said Liu.