Nearly 700,000 Muslims have fled country to Bangladesh due to persecution by military and Buddhist mobs, with more still fleeing.
President Rodrigo Duterte says he told Ms Suu Kyi to ignore the human right activists, describing them as a “noisy bunch”.
The two met in New Delhi this week at a summit of south east Asian leaders on the 25th anniversary of ASEAN-India ties.
President Duterte was speaking at a meeting of the Philippines-India Business Forum in New Delhi on Friday.
Nearly 700,000 Rohingya Muslims have fled persecution by Myanmar’s military and attacks by Buddhist mobs into Bangladesh.
Though Ms Suu Kyi has been the de facto head of Myanmar’s civilian government since her party swept elections in 2015, she is constitutionally limited in her control of the country and the military is in charge of the operations in Rakhine.
Still, Ms Suu Kyi has faced widespread international criticism for not speaking out in defence of the Rohingya, especially given her history as a Nobel Peace Prize winner.
Former New Mexico Gov Bill Richardson resigned suddenly from an advisory panel on the crisis this week, calling it a “whitewash and a cheerleading operation” for Ms Suu Kyi.
“I pity her because she seems to be caught in the middle being a Nobel Prize winner for peace and this,” Mr Duterte said.
“We are talking about our country, the interest of our country, our own country, and I said, ‘Do not mind human rights (activists). They’re just a noisy bunch’,” he added.
President Duterte is a regular target of criticism for his deadly war on drugs, which has left thousands dead over the past 18 months amid allegations of extrajudicial killings by police and other rights abuses.