The raids led to the arrest of nine suspected members of the Islamic network in the Jakarta area and at Semarang in Central Java.
"It's true there is a document," national police spokesman Basyir Barmawi told reporters.
But when asked whether the Marriott was on that target list, Barmawi said he had not read the document in detail and much about it remained uncertain. He said police still had to confirm who produced it "and all sorts of things".
Police said "about five" political leaders, high-profile individuals and several shopping centres were listed as targets in the seized documents.
The bombing of the US-owned Marriott Hotel in Jakarta is the latest in a series of attacks in Indonesia over the past year that have left hundreds dead and injured.
No-one has yet claimed responsibility. And with Indonesian authorities battling several militant groups simultaneously, the spotlight of blame may fall on more than one suspect.
Tuesday’s hotel bombing comes just two days before a verdict is expected in trial of an Indonesian Islamist, Amrozi Bin Nurhasyim.
A member of the outlawed Jama Islamiyyah network, Amrozi is accused of masterminding the deadly Bali attacks last October. The trial of the group's alleged spiritual leader, Muslim cleric Abu Bakar Ba'asyir, is also continuing in Jakarta.
One of the group’s top leaders, Riduan Isamuddin, also known as Hambali, remains at large. Hambali has been accused of bring Jemaah Islamiah’s link man with Usama bin Ladin's al-Qaida network.
As a result, the Jama Islamiyyah group tops the list of suspects behind the Marriott bombing. The target is a well-known meeting point for Westerners fits the group’s believed pattern of behaviour.
The Indonesian authorities are also fighting separatist rebels in the province of Aceh, which has been under martial law since May.
Fighting in the province has grown increasingly brutal in recent months with both sides accusing the other of atrocities and terrorist attacks.
Pro-government paramilitaries have been accused of human rights activists of killing civilians indiscriminately.
JI attack timeline
12 October 2002:
Bali bomb attacks kill 202 (mainly tourists), hundreds injured
5 December 2002:
Three killed in blast at a McDonald's restaurant
3 February 2003:
National police headquarters in Jakarta bombed, no casualties
27 April 2003:
A bomb explodes at Jakarta's main airport, injuring 11
14 July 2003:
A bomb rocks parliament after nine Islamist militants arrested. No casualties
5 August 2003:
Fourteen killed, 150 injured in Jakarta hotel bombing
The Free Aceh Movement (GAM) has been blamed for a 27 April bomb blast on a Kentucky Fried Chicken restaurant at Sukarno-Hartta International Airport. GAM has denied it was responsible.
However, an attack on the Marriott, which carries a high risk of foreign casualties, des not seem a logical tactic for GAM, which has sought international help for its cause.
Dissident military elements
Pro-government paramilitaries have attracted negative publicity not only in Aceh but in another separatist struggle – that of East Timor.
Annexed by Indonesia in 1974, East Timor’s struggle for independence descended into shocking bloodshed in 1998, with pro-Jakarta militias widely accused of massacring civilians. Indonesian army officers were later put on trial for human rights violations.
Coincidentally, within hours of the Marriott hotel attack, the verdict in another prominent court case was delivered.
A special human rights court sentenced Major-General Adam Damiri to three years in jail for failing to stop the atrocities during East Timor's 1999 independence vote.
Indonesians are aware some hardline elements in the armed forces are angry that Major-General Damiri, as well as 17 other Indonesian soldiers and officials, were put on trial.
With presidential elections due next, the Tuesday’s bombing might have served as a blow intended to damage the incumbent regime’s credibility.