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To many Dutchmen, the idea of parting with Indonesia was shocking. Many Dutch thought their country had a mission to develop Indonesia. The Indonesian wish for independence to many Dutch came as a complete surprise. Because Indonesian nationalists, which had no electoral or official legitimacy—save ethno-state nationalism, under Sukarno cooperated with the Japanese, they were branded as traitors and collaborators. Almost every Dutch political party was against Indonesian independence. The Protestant Anti-Revolutionary Party (ARP) were very supportive of the Dutch Ethical Policy in Indonesia. The newly established liberal People's Party for Freedom and Democracy campaigned for a hard-line policy against the nationalists. Even the Labour Party, which supported Indonesian independence in principle, was hesitant, because of the policies of Sukarno.

Minister of Colonies Jan Anne Jonkman defended the Linggadjati Agreement in Parliament in 1946 by stating that the government wished for New Guinea to remain under Dutch sovereignty, arguing it could be a settlement for Eurasians. A motion entered by the Catholic People's Party (KVP) and the Labour Party, which was accepted by parliament, stated that the declaration of Jonkman in parliament should become a part of the Linggadjati agreement. Duly accepted, the Netherlands thus unilaterally 'amended' the Linggadjati agreement to the effect that New Guinea would remain Dutch. Labour parliamentary group leader Marinus van der Goes van Naters said afterwards the Labour Party entered the motion with the KVP because it feared the Catholics otherwise might reject the Linggadjati agreements.

The Indonesians did not accept this unilateral amendment. In order not to jeopardise the scheduled transfer of sovereignty, the Indonesian vice-president Mohammad Hatta offered to maintain Dutch sovereignty over New Guinea for one year and reopen the negotiations afterwards.[citation needed]