Battles were still fought on the Moluccas until well into the 1960s by RMS guerrilla fighters, led by president dr. Chr. R.S. Soumokil, Esq. He was captured in 1963 by the Indonesian army. After his execution in 1966, J.A. Manusama B.Sc. established a government in exile and succeeded Soumokil as president.

The execution of Soumokil in 1966 led to the first violent act by Moluccan youths in the Netherlands, who set fire to the Indonesian embassy in The Hague. More protests in the battle for a free RMS (Republik Maluku Selatan) ensued in the years that followed.

Best known are the occupation of the Indonesian ambassador's residence in Wassenaar in 1970, and the train hijackings near Wijster in 1975 and De Punt in 1977. These protests left behind deep wounds in Dutch and Moluccan society.