The allegations revolve around possible irregularities within the organization, which for years received millions of euros and multiple properties from private donors.
A 19-year-old boy who was benefited from the NGO, accused one of its leaders of sexual abuse, and also a former employee of the organization said he was fired for denouncing abuse against three youngsters.
Its founder, Father Antonios Papanikolaou, rejected the accusations.
Since its creation, the NGO received numerous awards, including the European Citizen Award in 2018, which rewards individuals or entities that promote integration and tolerance.
This week, the government changed the entire board of directors and management of L’Arche du Monde.
The children are safe, Greek Prime Minister Kyriakos Mitsotakis, speaking to Alpha TV, said.