The Nigerian soldier will go into isolation at a "calamity unit" at the University Medical Center Utrecht, according to Inge Freriksen.
He is expected to arrive in Amsterdam over the weekend and be transferred by ambulance to nearby Utrecht.
Late Thursday, the UN mission announced that the soldier had tested positive for the dreaded disease a day earlier. This is the third case of Ebola among mission personnel, according to Karin Landgren, the top UN envoy in the country. The previous two died.
The man will be the first Ebola patient hospitalised in the Netherlands. He is being treated in a Dutch hospital at the request of the World Health Organisation, Freriksen said.
The Ebola outbreak has sickened nearly 17,300 people, mostly in Guinea, Liberia and Sierra Leone. Of those, about 6,100 have died.
The UN force, with about 7,700 troops and police, has been in Liberia since 2003 to bring stability after two civil wars.