"We are neighbours, and we have to work in such a way so that we can make compromises," Jouwe told reporters after talks with Welfare Minister Aburizal Bakrie.
"It's time that we worked together," said Jouwe, who created the banned "Morning Star" flag, a symbol of the separatist group.
The OPM has been fighting a sporadic rebellion in Papua, formerly Irian Jaya, since the early 1960s.
Jouwe said his overtures did not necessarily mean that he gave up the struggle for an independent Papua.
His son, Nicolaas Alexander, said: "He did not come here to surrender his ideals but to hold dialogue."
Bakrie said the government was committed to improving the welfare of Papuans through education, better infrastructure and affirmative action.
Jouwe's visit to Jakarta came amid a spike in violence in Papua.
A soldier and two civilians were shot and killed this month in attacks blamed on the rebels. In January, insurgents armed with sickles and arrows raided a police post and stabbed the wife of an officer before making off with four guns and ammunition. Police arrested one person for that attack.
Papua, a predominantly ethnic Melanesian province 3,700 km northeast of Jakarta, is a former Dutch colony that became an Indonesian province in 1964 after a vote involving tribal leaders that many regarded as a sham.