The withdrawal on Thursday marked the final stage in a pullout of tens of thousands of Indonesian soldiers and police reinforcements from Aceh under the peace agreement between rebels and government forces.
On Thursday, 2150 policemen jostled to board a warship in the city of Lhokseumawe after nearly a week stuck in a port compound.
Mulyatno, Lhokseumawe police chief, said the last withdrawal left around 9000 policemen in Aceh.
The peace deal
The Finnish-mediated peace deal ended nearly 30 years of war that took some 15,000 lives, most of them civilian, in the province on the northern tip of Sumatra island.
The agreement was signed in August after talks between the two sides accelerated after the tsunami a year ago, which left 170,000 people dead or missing in Aceh.
The 15 August truce requires Indonesia to cut troop and police levels in Aceh to no more than 14,700 soldiers and 9100 police.
Before the pact, it had more than 35,000 soldiers and 15,000 police in the province.
The Free Aceh Movement finished its weapons handover earlier this month.
With the handover now complete and troop withdrawals concluded, security experts say the next challenges are finding jobs for demobilised fighters and satisfying rebel demands for political participation in Aceh.