A police source said the three men were arrested at 4am this morning from a house in Cimanggis, Depok.
"They were sleeping when we arrived there," the police officer said.
He said police seized two bags and some books but they were not analysed right away as it was still dark.
Indonesia's MetroTV broadcast footage of the handcuffed men being escorted by police.
The officer said the men had told police they were employees at a building material shop in Depok.
They are currently being held at the Depok police station.
The area near a Starbucks coffee shop where the attack by suicide bombers and gunmen began remained cordoned off with a highly visible police presence Friday.
Onlookers and journalists lingered nearby, with some people leaving flowers and messages of support.
A large screen atop the building that houses the Starbucks displayed messages that said "#prayforjakarta" and "Indonesia Unite".