But Mr Jouwe did not renounce the independence movement and referred to Indonesia as a "neighbouring country".
"We need to have a dialogue with Indonesia because we are two nations that upheld our identity and kept it for so many years," he said.
After meeting political leaders in Jakarta, Mr Jouwe arrived in the Papuan capital of Jayapura yesterday accompanied by Indonesian officials.
A large contingent of police prevented independence activists, who were there to greet him, from making contact and unfurling the Morning Star flag, the symbol of resistance from the region's Melanesian people.
Mr Jouwe is credited with designing the distinctive flag, which is banned in Indonesia. Activists caught raising the flag face up to 10 years' prison. The OPM, which Mr Jouwe co-founded, is also banned.
On Friday Mr Jouwe met Indonesia's Welfare Minister Aburizal Bakrie, who signalled Jakarta's readiness to forge a new autonomy agreement and said the country needed to "pay more attention" to the region, formerly part of the Netherlands East Indies that was not handed over with the other territories that became Indonesia in 1949. The Dutch handed Papua to Indonesia in the 1960s under US pressure, part of a Cold War geo-political move to win over Indonesia, whose President Soekarno had been acquiring arms from the Soviet Union and moving closer to Indonesia's communists.
A United Nations-sponsored referendum in 1969 to confirm Indonesian sovereignty was criticised as a sham because only 1000 hand-picked Papuans cast votes in a ballot that overwhelmingly endorsed Indonesian rule.
Papua was granted special autonomy in 2001, but its development has been slow and living standards remain the lowest in the country.
A belief that its wealth is being siphoned off by the central government has underpinned the grievances of indigenous Papuans, though a 2001 autonomy scheme diverted more resource royalties to its provincial governments. Under a policy of internal migration the region has been swamped by Indonesians, prompting further resentment.
Tensions have been on the rise in Papua in recent months, with the poorly equipped military wing of the OPM having several skirmishes with the Indonesian military, including one raid that killed an Indonesian soldier a week ago.
Police last week offered a reward for the capture of Goliat Tabuni, the OPM military chief. Victor Yeimo, chairman of the West Papua National Committee, an organisation for independence activists, said there had been an increase in Indonesian military activity, prompting Mr Tabuni to flee to the mountains.