A leadership row has erupted in the Philippine House of Representatives, delaying President Rodrigo Duterte’s delivery of his annual state of the nation address.

The storm also held up the passage of crucial Muslim autonomy legislation aimed at ending one of Asia’s longest Muslim rebellions.

As Mr Duterte arrived in a helicopter in the congressional complex, representative Gloria Macapagal Arroyo, backed by dozens of allied legislators, took the main seat in the centre stage of the House’s plenary hall in a sign that she was taking over the post of house speaker Pantaleon Alvarez.

Ms Arroyo, a former president, tried to speak from the stage during the dramatic stand-off but her microphone was turned off. She tried to shout, apparently to explain what was happening, but later stepped down from the stage, waving at the crowd.

Gloria Macapagal Arroyo
Gloria Macapagal Arroyo bangs the gavel after taking the oath as the new house speaker, sparking the row (AP)

Mr Alvarez, along with senate president Vicente Sotto III, fetched Mr Duterte and led the visibly confused leader to a holding room as the dispute over house leadership unfolded in the packed chamber.

Mr Alvarez and Ms Arroyo are close Duterte supporters in the 292-member House, which is largely dominated by the president’s allies.

Opposition senator Risa Hontiveros said: “They chose to disrespect their own president and attend to their own ambitions in full view of the nation. For almost an hour, it seemed that nobody was in control.

“This is the true state of the nation. It is petty infighting, backstabbing, and brinkmanship, all done at the people’s expense.”

The Philippines parliament
The move sparked angry and confusing scenes in the chamber (AP)

Others called the squabble a “circus” that bared a deep crack in Mr Duterte’s ruling coalition. Some representatives said they would not recognise Ms Arroyo’s rise to the House speakership based on a resolution signed by more than half of the House membership in a sign that the political tug-of-war would drag on.

An arrangement was later reached allowing Mr Alvarez to lead the joint session with Mr Sotto to break the impasse, which delayed the president’s speech for more than an hour.

The leadership row earlier prevented the House from ratifying a Muslim autonomy bill that was part of a peace deal with the 11,000-strong Moro Islamic Liberation Front.

Mr Duterte had been expected to sign the autonomy bill into law on Monday and highlight it in his speech.

The peace deal, which he promised to sign within 48 hours, is a bright spot in his two-year presidency, which has come under heavy criticism over his human rights record, deadly anti-drug crackdown and vulgar language.

Rodrigo Duterte
Demonstrators burn an effigy of Rodrigo Duterte (AP)

“I make the solemn commitment that this administration will never deny our Muslim brothers and sisters the basic legal tools to charter their own destiny within the constitutional framework of our country,” Mr Duterte said.

He added: “We will need loads of understanding and patience to endure and overcome the birth pangs or pains of the new beginning.”

Thousands of flag-waving protesters rallied outside the House and burned his effigy. They condemned him for the drug killings and for failing to ease poverty and inflation.

Aside from the Muslim autonomy pact, Mr Duterte reaffirmed his resolve to fight illegal drugs and introduced a draft constitution that would shift the country to a federal system of governance.

The moves, including opening the country’s 1987 constitution to amendment, have been opposed by several groups and opposition politicians, who fear they are designed to prolong Mr Duterte’s rule and give him dictatorial powers.