Later he was transferred to Java where he suffered Japanese occupation during the World War II.

In response to the attempts of centralization by the government in Jakarta, the initiative was taken to withdraw the Daïra of South Moluccas from the federation.

On April 25, 1950, at the initiative of Chris Soumokil and Johan Manusama, the independent Republic of South Moluccas (in Indonesian, Republik Maluku Selatan) was proclaimed by a declaration signed by Johanis Manuhutu and Albert Wairisal.

In early 1952, Manuhutu was captured by the Indonesian army in an operation on Seram Island, and was sentenced to five years in prison.

He reconciled with the Indonesian authorities and in 1970 he may have been involved in discussions about the possible return of Ambonese people from the Netherlands.