Police detain more than 50 people, but protests over disputed vote said to be over.
“The president and the prime minister do not want to put Port Gentil under a state of siege. We are not yet at that level,” Ndongou said.
“But if peace, order and harmony are not restored, we are going to solicit authorisation to do so from parliament.”
Port Gentil is already under a dusk-to-dawn curfew, but a state of emergency can be called only after cabinet and parliamentary discussion.
A club run by Total, the French oil company, and the French consulate in Port Gentil were torched.
French paratroopers are guarding the consulate and Total has evacuated its staff to Libreville, the capital.
Some opposition supporters believe that France helped Bongo, 50, to fix the election, allegations that both Paris and Bongo have denied.
Ndongou said that none of the deaths were caused by the military and that the government would accept an international investigation into the clashes.
In Libreville, the capital, where tensions had abated, Bongo, the son of the late leader Omar Bongo, made his first appearance since the election.
He appealed for calm and urged his rivals to take their allegations of fraud in the August 30 poll to court.
Opposition leaders have said that they will legally contest the election results.
Bongo received 41.7 per cent of the vote compared to about 25 per cent each for his closest rivals Andre Mba Obame, the former interior minister, and Pierre Mamboundou, a veteran opposition leader.
Omar Bongo died in June after 41 years of rule.