Not all of Dutch New Guinea was occupied by the Japanese. Large parts of the interior and the southern coastal area near Merauke remained free of Japanese troops. In April 1942 and the months that followed the Japanese did occupy the western area called Vogelkop and the northern coastal areas. Initially this area came under the authority of the Japanese Navy; in October 1943 it was passed to the 2nd Army group.
On 12 April 1942 the Japanese occupied Manokwari, the main town of the section West and North New Guinea. They took few prisoners in and around Manokwari, and they interned few civilians. The majority of the European civilians in this area had already been evacuated to Australia by the DEI authorities. Members of guerrilla groups that were later captured by the Japanese, were nearly all executed. The prisoners and internees that had fallen into Japanese hands in Manokwari, or had been brought there from other locations on occupied New Guinea, were transported to Ambon fairly quickly – in late April and mid-August 1942 respectively.
Hollandia had only had a small administrative post until the Japanese occupation. On 13 April 1942 Hollandia was occupied by the Japanese. The few Dutch officials who were still there were interned with their families about 13 kilometres inland, in the Field police station in Joka, were later taken to Manokwari and subsequently transported to Ambon.
Starting in February 1944 the station in Joka served as an internment location for a group of about 100 predominantly German missionaries and nuns, who came from the north coast of Australian New Guinea. This group originally consisted of some 200 people. The boat that had taken them to Hollandia had been bombed by American airplanes on the way over, which had killed about half the internees. The camp in Joka was liberated on 2 May 1944, a few days after the allied landing at Hollandia.
As the allies drew nearer, a large number of natives, Chinese immigrants, Indo-European colonists and also Moluccan and Menadonese heihos, all considered untrustworthy, were interned two primitive camps in the hinterland of Manokwari. Both camps were located on the Prafi river: one camp about 35 km northwest of Manokwari on the estuary of the river, the other approximately 20 km southwest of Manokwari on the lower reaches of the river. In total more than 900 people were interned here: men, women and children. At least 400 of them, and perhaps substantially more, died before the camp was liberated in November 1944.