Thousands of people belonging to a powerful local indigenous Christian organization occupied a busy portion of the main highway in Manila on Friday to protest what they allege to be government's meddling over internal affairs of their church.

Members of Iglesia ni Cristo (Church of Christ) or INC also called for the resignation of Justice Secretary Leila de Lima, who was investigating an illegal detention case filed by a dismissed churchminister against Iglesia's leaders.

Waving church flags and holding anti-government placards calling for religious freedom, Iglesia members chanted "Hustisya" (Justice) and "INC" as they blocked two busy intersections, causing late Friday night traffic jams.

Some 1000 church members began their protest by trooping to the Justice department on Thursday, even blocking de Lima's car from leaving the agency's premises, according to media reports.

On Friday, the members took their peaceful protest to the main EDSA highway, site of several demonstrations in the past including "people power" revolts that toppled two presidents.

"This is a display of INC solidarity," a member who joined the protest on the highway and who gave his name as Ka Vic told Reuters. "We responded to the call of our church leaders. The government should respect the separation of church and state."

Some members questioned the government's moves to probe infighting in the Iglesia when it has yet to bring justice to 44 elite police force members killed during a firefight with Muslim rebels in January. Two of the policemen who died were Iglesia members.

Police declined to give an estimate of the crowd that occupied the highway, but organizers were hoping to gather 50,000 members until Monday, a public holiday.

Presidential spokesman Herminio Coloma Jr said in a statement "the government does not wish to interfere in the internal affairs of any legitimate organization," adding it was not taking an adversarial position against the Iglesia.

Interior Secretary Mar Roxas said police will exercise maximum tolerance over the crowd but stressed people's right to peaceful assembly should not cause inconvenience to others.

Political analysts said the protest was a show of force by the estimated 2-million-strong Iglesia, an influential group that politicians have courted in the past for votes. Iglesia members are widely known to follow their leaders' advice and vote as a bloc. The next presidential polls is set for May 2016.

About 80 per cent of the country's 100 million people are Catholic, with the rest comprised of Muslims and Christian groups including home-grown churches, the biggest of which is the Iglesia.