Patek will be charged under the country's criminal code instead of the law on terrorism, which can't be applied retroactively, National Police spokesman Inspector General Anton Bachrul Alam said.
The law was enacted in 2003, a year after the bombing.
Under the criminal code, police could charge Patek with premeditated murder and also charge him in relation to explosive use under Indonesia's emergency law on explosives, Alam said.
But Patek, 41, still faces the death penalty if convicted.
Patek allegedly made the explosives that were detonated in the 2002 Bali bombing.
He was arrested by Pakistani authorities in January for a violation of the country's immigration laws and was deported to Indonesia Thursday.
"He is now at Kelapa Dua Police Detention Center awaiting further investigation," Alam said.
Anton declined to comment whether Patek had met al-Qaida leader Osama bin Laden who was killed this year in a U.S. military operation in Pakistan.
"We still don't know. He has just arrived," Alam said.
The Bali bombing in October 2002 was the deadliest act of terrorism in the history of Indonesia. More than three dozen Indonesians died and more than 150 of the 202 dead were foreigners, including 88 Australians. Around 240 people were injured.
Three bombs were detonated -- a backpack-mounted device carried by a suicide bomber, a large car bomb and a third smaller device detonated outside the U.S. consulate in Denpasar, causing only minor damage.
Patek is believed to have links with the outlawed Jemaah Islamiah, the militant group blamed for the Bali attacks and whose main leader was Dulmatin, killed by Indonesian security forces in March last year.
Dulmatin, 40, was one of Indonesia's most wanted men for his suspected part in the bombings in the tourist district of Kuta on the southern Indonesian island of Bali. The United States had placed a $10 million reward for capture of the elusive militant. He was shot by police while in an Internet kiosk in the Jakarta suburb of Pamulang City.
Patek, born on the Indonesian island of Java, had a $1.5 million reward for his arrest offered by the U.S. State Department Rewards For Justice Program.
Aside from his involvement in the Bali bombing, Patek is an important prisoner because of information he may have about terrorist networks in South Asia.
"Umar Patek is critical to understanding the terrorist networks in South East Asia," Sidney Jones of the International Crisis Group, told the BBC when Patek was arrested. "And because he appears to have been arrested in Pakistan, he's also going to be critical to understanding the networks between South Asia and Southeast Asia.
"He's in a position to know more than almost anyone else in the region exactly what the strengths, networks, contacts, finances and so on of each of these groups is," Jones said.