Rois, alias Iwan Darmawan, was reportedly arrested on 10 November at a railway station on the western tip of Java island, the report said on Tuesday.
Police did not publicise the arrest while they confirmed the suspect's identity, the report said.
But when asked about the report, General Dai Bachtiar refused to confirm or deny it.
"I can say that some suspects in the latest bombing have been arrested," he said, after meeting President Susilo Bambang Yudhoyono.
"But I can't elaborate at this time. I will explain at the appropriate time."
Darmawan played a key planning role in the 9 September attack on the Australian Embassy, which killed 10 people including one attacker, the newspaper Kompas quoted the police source as saying.
Report said Darmawan was also
involved in the Bali bombings
Police announced they were hunting for Darmawan two weeks after the embassy attack.
They said then he was believed to be on the run with the attack's alleged masterminds, Malaysian nationals Azahari bin Husin and Noordin Mohamed Top.
The Kompas report said Darmawan was arrested with five other people, but gave no more details.
It also said Darmawan was involved in the Bali bombings, which killed 202 people, most of them foreign tourists, and a car-bomb attack on the JW Marriott Hotel that killed 12 people.
Police have arrested scores of suspects in three attacks, two of whom have been sentenced to death. All have been blamed on Jemaah Islamiya, a Southeast Asian group which is accused of having links to al-Qaida.