In a move criticised by rights activists, lawmakers slashed the budget of the Commission of Human Rights that has been at loggerheads with the Duterte administration.
Fighting in Marawi City has entered a fifth week and nearly 350 people have been killed.
Duterte’s plan is unlikely to sit well with China, which lays claim to almost all the South China Sea, especially as it comes amid a fast-warming relationship in recent months.
The protesters condemned the deadly narcotics crackdown, which has killed about 7,700 people since the firebrand leader came to power on June 30.
Philippine and US military officials agreed to reduce joint exercises and US troop deployments, and focus more on non-traditional military training.
Saying that the presence of Americans gives the ISIS-linked Abu Sayyaf targets in the Philippines, Duterte said he wanted the US Special Forces out.
The wave of killings unleashed since President Duterte came to power has alarmed rights groups and brought expressions of concern from the US, a close ally.
On Monday, dozens of Philippine officials went to the national and regional police offices to clear their names, fearing the president’s order to hunt them down if they failed to surrender within 24 hours.
The fishermen currently face clashes with Chinese boats and hope that a favourable verdict will pressurise China to grant access.
More than 40 suspects have been killed since Rodrigo Duterte won elections with his promise of tackling drug-related crime and strong advocacy of extrajudicial killings.