President Barack Obama said Wednesday US military efforts to contain Ebola would give way to a civilian-led drive to "extinguish" the deadly virus, as he ordered home American troops in West Africa.

"We are shifting our focus from fighting the epidemic to now extinguishing it," Obama said, flanked by Ebola response staff.

Obama said a military force that peaked at 2,800 troops would number not more than 100 by the end of April, though he was at pains to stress that it was not a case of job done.

The forces, most of whom were stationed in Liberia, constructed Ebola treatment units, trained health workers, provided logistical support for aid agencies and set up labs to test blood samples.

"We have risen to the challenge" Obama said.

Guinea and its neighbors Sierra Leone and Liberia have registered more than 9,000 deaths since the Ebola epidemic flared up in December 2013.

After months of decline, the World Health Organization on Wednesday reported the number of new cases rose for the second week running, including a "sharp increase" in Guinea.

"Guinea reported a sharp increase in incidence, with 65 new confirmed cases compared with 39 the week before," the WHO said in a report.

Obama was careful not to declare the fight against Ebola as "mission accomplished."

"I want to be very clear here, while our troops are coming home, America's work is not done. Our mission is not complete."

Liberia, he said, "has seen the best progress, Sierra Leone is moving in the right direction, Guinea has the longest way left to go.

"Our focus now is getting to zero.

"As long as there is even one case of Ebola that is active out there, risks still exist. Every case is an ember that if not contained could light a new fire."

The United Nations played down the impact of the US troop withdrawal.

"This departure does not leave a hole," UN coordinator David Nabarro told AFP.

He stressed that 10,000 American civilians are engaged in hardest-hit Liberia, Guinea and Sierra Leone.

"I hope that they will continue to be engaged and to provide cash and material and elements until the thing is finished," Nabarro said.

The United States has set up a reserve force from the National Guard that could return to West Africa quickly to deal with an upsurge, added Nabarro.

He said rebuilding health systems and getting economies back on the road to recovery was also part of the task at hand.

"I am hopeful that we will see zero (cases) in Liberia quickly... But Liberia is not going to be safe until Guinea and Sierra Leone are also free. I am truly hopeful that we will see that this year," he said.