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Patek, who was captured in January after almost a decade on the run, arrived in Jakarta on Thursday morning aboard a specially chartered flight from a Pakistani airforce base.
He was immediately taken to the Police Mobile Brigade Headquarters at Kelapa Dua, on the outskirts of Jakarta.
Indonesian Police spokesman, Inspector-General Anton Bachrul Alam, said Patek's standing as a "high-value" prisoner meant security for his transport from Pakistan to Jakarta was extremely tight.
"We prepared tight security because Umar Patek is a terrorist figure," he said.
"We have to be always ready and alert."
Patek, long suspected of having built the bombs for the 2002 Bali nightclub attacks which killed 202 people including 88 Australians, is likely to face charges of murder and possession of explosives.
Indonesia's counter-terrorism chief, Ansyaad Mbai, while not going into detail, confirmed that the 41-year-old had already admitted involvement in the Bali attacks as well as other terrorist activities.
Patek, who was captured on January 25 in Abbotabad, the same Pakistani city where al-Qaeda leader Osama bin Laden was killed by US forces in May, is believed to have made the admissions when a team of Indonesian intelligence officers interrogated him in June.
"He acknowledged that he (was) involved in the first Bali bombing and involved in the Christmas bombing," Mr Ansyaad said, referring to bombings of churches in a number of Indonesian cities on Christmas Eve in 2000.
"He has many role in terrorist act in Indonesia," Mr Ansyaad added.
He told AAP that Patek had also provided vital information about networks in Indonesia.
Indonesian officials have indicated that their chances of pursuing a case against Patek were limited because counter-terrorism laws introduced in 2003 could not be applied retrospectively.
But Mr Ansyaad said authorities would instead seek to prosecute Patek under the criminal code, on charges of "murder" and possession of explosives.
"He cannot be prosecuted by the terrorism law (because) our terrorism law cannot be retroactive. But it doesn't mean that Umar Patek cannot be prosecuted in Indonesia," he said.
Patek is also wanted in the Philippines, where he allegedly plotted deadly attacks with local militants after fleeing Indonesia following the 2002 bombings.
Officials in Manila confirmed last month that Pakistan had also offered to deport Patek to the Philippines.
The possibility of Patek facing trial in Australia had also been considered, Australia's counter-terrorism ambassador, Bill Paterson, said in May during a visit to Jakarta.
Australian officials are expected to seek a briefing on Patek's extradition.
"The primary goal for Australia and Indonesia is that justice is done," a spokesperson for acting Foreign Minister, Martin Ferguson, said on Thursday.
"Australia has been, and will continue to be, in contact with Indonesian authorities on the matter of Umar Patek."
"It would not be appropriate to comment further due to the sensitivity of the case and the prospect of legal action in Indonesia."
But the spokesperson said the Australian government welcomed the extradition and was confident in Indonesia's ability to prosecute a case against Patek.
"Indonesia has had an impressive track record in the successful prosecution of suspected terrorists under its criminal laws, most recently Abu Bakar Bashir," the spokesperson said.
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