He said a parked motorcycle found in the rubble had a bomb on it.
Ronaldo Puno, the interior secretary, also said the target appeared to be Akbar.
He sought to downplay the possible involvement of Muslim fighters, saying the investigation is "pointing away from terrorist attack and more of a directed assault on a certain individual".
Suspected Abu Sayyaf links
Akbar, 47, was a member of the Moro National Liberation Front, a Muslim separatist group that dropped its secessionist goal and signed a peace accord with the government in September 1996.
He was suspected of knowing the leaders of the Basilan-based Abu Sayyaf and later having a falling out with the group's commanders.
As governor of southern Basilan province, he had supported US-backed military operations on the island targeting the group.
The government calls the Abu Sayyaf "terrorists" and has blamed them for many bombings in the country.
Tuesday's explosion ripped through one entrance of congress just minutes after its evening session ended around 8pm (1200 GMT), sending debris flying across the parking lot.
The driver of another legislator and a congress employee were also killed in the blast which tore the roof off the southern entrance of the building.
Seven people, including at least two congresswomen, were injured.
Joel Villanueva, a congressman, said less than 50 of the 275 members of the house were inside when the bomb exploded.
"It was a very huge explosion," Villanueva said. "We are stunned."
Gloria Arroyo, the president, was to face a new impeachment complaint set to be debated in congress on Wednesday morning.
Ortigas said many Filipinos, long suspicious of the Arroyo administration, felt the government was involved in many tactics to divert attention from allegations of corruption against the president and some felt the blast may be another such tactic.
Arroyo, facing her third impeachment complaint in as many years, said while police investigated and bolstered security, "we're making a call against rumours, accusations that create confusion, fear and conflict".
The Philippine capital has been jittery since a blast tore through a shopping mall in Manila's financial district last month, leaving 11 people dead and injuring over 100.
Police initially thought a bomb was to blame, but later said the explosion was an industrial accident.
The owners of the mall disputed that finding and a red alert is up over the city once again.