Mabanta said the police accepted the offer of the specialist squad, but then did not use it in resolving the hostage-taking.
"The Light Reaction Company which we presented as a very viable alternate is highly-trained, highly-equipped, standards coming from the U.S. armed forces," he told a media briefing.
"It's specialty is hostage-taking and release of hostages."
The police have said there had been defects including poor handling of the negotiations, and that the assault team was inadequately trained, equipped and led.
Light Reaction squads are used to fight Islamist militants of the Abu Sayyaf group in the southern Philippines, Mabanta said.
On Wednesday, Chief Superintendent Rodolofo Magtibay, the head of police in area of the capital where the bloody siege took place, stood down while it was investigated. A police spokesman had said Magtibay was the ground commander.
On Thursday, Magtibay told a Senate inquiry he had not called for extra help as he thought the SWAT team could handle the situation.