Troops backed by army helicopters and UN police and armoured personnel carriers scoured the outskirts of the capital Dili, combing through the jungle in search for the suspected attackers.
"The hunt is ongoing ... These warrants are valid for 21 days and will be handed to the police for execution," Longuinhos Monteiro, the prosecutor-general, said on Thursday.
'Persons of interest'
Major Phil Pyke, an Australian military spokesman, said the operation was launched after a "group of persons of interest were identified" around the village of Dare.
It was not immediately clear whether anyone was detained.
Jose Ramos-Horta, the president, was shot on Monday by suspected rebels as he was returning from an early morning walk on the beach, leaving him seriously wounded.
An hour later a convoy carrying Xanana Gusmao, the prime minister, was ambushed but he escaped unhurt.
Ramos-Horta, 58, currently in an induced coma after having undergone three rounds of surgery, is recovering in an Australian hospital.
"He remains in a serious but stable state," Stephen Smith, Australia's foreign minister, told parliament on Thursday. "In these circumstances, stability means progress."
Brigadier-General Taur Matan Ruak, East Timor's military leader, has strongly criticised the international forces for failing to prevent the daring attacks.
Reinado, suspected of staging Monday's attacks against Ramos-Horta, was killed during an exchange of gunfire with presidential guards.
Hundreds of mourners gathered at the funeral of Reinado and a second rebel killed during Monday's shootout.
Reinado, a former army officer, was a leading figure in the unrest in May 2006 that destabilised the country, which gained independence in 2002.
|Hundreds of mourners gathered |
for Reinado's funeral [Reuters]
International peacekeepers were dispatched to restore calm following violent clashes on the streets of Dili.
Al Jazeera's Step Vaessan said that many people in Dili still see Reinado as a hero.
"He has quite a lot of popular support among students, among the normal population ... because he was seen as someone who was fighting for their cause," she said.
"There is a lot of disatisfaction in East Timor about the leadership."
Meanwhile, Kevin Rudd, the Australian prime minister, is scheduled to visit Dili on Friday in a show of support for the government, the Australian foreign minister said.
Stephen Smith said Rudd will hold talks with Gusmao in the capital to relay "all the things that I have outlined to the house".
He said the situation in Dili was "tense but calm" and hoped that it will remain so.