The minister made the statement right ahead of the final round of peace talks between the GAM and the government scheduled for later this month.
"They must give their weapon to the TNI (armed forces)," said Juwono.
He stressed that the mechanism of handing in weapons and the withdrawal of the government troops from the rebellious Aceh Province must be seriously discussed in the upcoming fifth round of meeting in Helsinki, Findland on July 12.
The troops would be pulled out from the province after both sides reached an agreement, he said.
"The informal meetings have not discussed about the troops withdrawal. As long as there is no agreement, we keep stationing our troops in the province," he added.
The minister said that the pulling out may be conducted, but he said that the GAM leaders in Sweden must be able to control their personnel in the field, whom have killed many Indonesian troops, the Media Indonesia said.
The Indonesian government and the GAM agreed to bring the settlement of the conflict to the negotiation table after the province was devastated by the tsunami on Dec. 26, 2004 which killed over 220,000 people and destructed some parts of Aceh province.
During the talks, the GAM agreed to diminish its demand for independence and proposed to a self-ruled government in the province.
The GAM has struggled for establishment of an independent state since 1976. Tens thousands of people have been killed in its conflict with the government troops.