Demonstrators, including Buddhist monks, shouted "Don't insult our country!" and "There are no Rohingya in Myanmar" in angry chants aimed mainly at the United Nations.
The migrant crisis in Southeast Asia has shone a spotlight on the dire conditions and discrimination faced by the roughly one million Rohingya in western Myanmar, a group widely seen as illegal immigrants from Bangladesh.
"This 1.3 million people are not from our country. I do not accept there is a Rohingya ethnicity here," said protester Kyaw Htet, 31.
More than 3,500 Bangladeshi economic migrants and stateless Rohingya Muslims from Myanmar have arrived on Thai, Malaysian and Indonesian soil in recent weeks.
The UN's refugee agency believes hundreds more could still be stranded at sea with diminishing supplies of food and water after a crackdown in southern Thailand disrupted a major human trafficking network.
Myanmar's navy last week found exhausted and hungry men and boys, mainly thought to be from Bangladesh, crammed in the rusting hull of a smugglers' boat off its coast.
But calls to help the group have stirred outrage among Buddhist nationalists, who have been increasingly prominent in Myanmar in recent years.
"Those helping the illegal migrant Bengalis are our enemies!" protesters shouted Wednesday in a sign of the depth of feeling on the issue among some in Myanmar.
At a press conference about its election plans Suu Kyi's opposition party sought to play down the problems in Rakhine, saying it was just one of many issues for the impoverished country to solve as it creeps out of the shadow of military rule.
"We know that we have to handle this problem some day," he said.
Noble Peace Prize winning opposition leader Aung San Suu Kyi has been reluctant to speak out on the migrant crisis. Observers say she fears alienating voters in the Buddhist-majority nation before elections in November.
