One of the five protesters, House of Representatives member J Virgilio Bautista, tried to hoist an anti-war banner as he left his seat but marshals seized it from him.
Bush, on an eight-hour state visit to the former US colony, was making the first address to the Filipino legislature by a US leader since Dwight Eisenhower in June 1960.
The legislators were all from fringe leftist parties and included Satur Ocampo, a former communist guerrilla leader.
A small number of Filipino legislators who opposed the US-led invasion of Iraq also wore pins that read "Legislators against War", but unlike the five they stayed to listen to the speech.
Bush told the Philippine Congress that the US would provide funding and technical assistance to modernise and reform the country's military.
But a senior administration official acknowledged on Friday that a pledge to provide refurbished combat helicopters had hit a funding snag.
"I'll be honest with you, we haven't found funding yet. I'm sure we will by the end of the next fiscal year, but we're not there yet," he told reporters on condition of anonymity.
Bush, after talks with Philippine President Gloria Macapagal Arroyo, also vowed to help bring the Muslim rebel group Abu Sayyaf "to justice".
He also pledged to provide development assistance to war-torn areas of the southern island of Mindanao once Manila established lasting peace with the Moro Islamic Liberation Front, the largest Muslim rebel group there.
"My government and yours are pursuing a common objective: We will bring Abu Sayyaf to justice. And we will continue to work together, along with our friends in Southeast Asia, to dismantle the Jemaah Islamiyah terrorist network and other groups that traffic in violence and chaos," Bush said, according to a text of his remarks.
Bush called on members of the Moro Islamic Liberation Front to "reject terror and move forward with political negotiations".
"When a lasting peace is established, the United States is prepared to provide our development assistance to Mindanao. Yet there can be no compromise with terror"
"When a lasting peace is established, the United States is prepared to provide our development assistance to Mindanao. Yet there can be no compromise with terror," he said.
Bush called the US-Philippine military alliance "a rock of stability in the Pacific" and said Washington and Manila agreed on Saturday to "update our defence cooperation".
He said the two nations have completed a review of the Philippine's security requirements and that Arroyo and her government have committed to a five-year plan to modernise and reform the military.
"I commend the president and your military leadership for taking this bold action. My country will provide technical assistance, field expertise and funding. But success requires more than American assistance.
Police block anti-Bush protesters trying to picket his speech
"Members of this body must invest in the Philippine military to ensure that your forces have the resources needed to win the war on terror and protect the Philippine people," Bush told the Philippine Congress.
Arroyo had deployed thousands of police and soldiers in Manila amid warnings from Abu Sayyaf that it would mark Bush's visit with violence.
There were also fears of retaliatory attacks from fighters sympathetic to the JI following the killing this week of top JI bomber Fathur Rohman al-Ghozi by Filipino troops.
Hundreds of riot police blocked a road leading to the House of Representatives, preventing about 7000 leftwing protesters from marching on the building.
The protesters burned several dozen flags, but there were no untoward incidents.