According to prosecutors Mohammad Jibril is suspected of having ties to the Jemaah Islamiyah group, which has been accused of carrying out a series of deadly attacks in Indonesia.
The indictment says Mohammad Jibril met Noordin Top, the former head of a Jemaah Islamiyah splinter cell known as "al-Qaeda in the Malay Archipelago".
After that meeting, it said Mohammad Jibril sent an e-mail to his brother, Ahmad Isrofil Mardhotillah, who was in the Saudi city of Mecca.
Mohammad Jibril and another suspect in the bombings, Syaefudin Zuhrithen, then flew to Mecca to arrange financing for the attacks, the indictment alleges.
|Noordin Mohammed Top was killed
in a police raid last year
Zuhrithen was later killed in a police raid.
The indictment did not specify how much money they raised and whether any reached Noordin.
Sidney Jones, a senior advisor for the Jakarta-based International Crisis Group, told Al Jazeera that Mohammad Jibril has "very strong connections in Pakistan" and had "almost certainly met with members of al-Qaeda" while he was there, but said the alleged links remained unclear.
"It may be that the police end up getting him on document forgery charges or immigration violations rather than on financing charges," said Jones, who has done extensive research on the al-Qaeda-linked Southeast Asian group Jemaah Islamiyah.
She said the alleged Saudi connection was also "very murky at this stage" because "as far as we know there has not been any Saudi money that has gone to previous bombings".
"We do know that there's been some financing for training in Mindanao [in the southern Philippines]… not from the Saudi government, but from individual Saudi donors," she added.
Since the hotel attacks, Indonesian police have arrested more than a dozen suspects including Al Khelawi Ali Abdullah, a Saudi citizen, accused of acting as a courier for funds from the Middle East used to finance the bombings.
His trial is expected to begin on Wednesday in Jakarta.
Noordin himself, the alleged mastermind of the attacks, was shot dead in a gun battle with Indonesian police at hideout in Central Java last September.
As well as having been blamed for the Jakarta attacks, Noordin is believed to have played a major role in four other bombings in Indonesia since 2002, including the nightclub bombings on the resort island of Bali that year that killed 202 people.
In a video in 2005, Noordin claimed to be al-Qaeda's representative in Southeast Asia and to be carrying out attacks on Western civilians to avenge Muslim deaths in Afghanistan.
The attack on the Jakarta Marriott was the second bomb attack to target the hotel.
A suicide bombing in 2003 left 12 people dead and injured more than 150.