The "Food Flotilla for Myanmar" arrived following a sweeping counterinsurgency campaign in Rakhine state, where most of the estimated 1 million Rohingya live. Last week, U.N. human rights investigators said it was "very likely" that Myanmar forces were guilty of crimes against humanity in the crackdown.
Organizers of the aid shipment say they trust the Myanmar government to deliver the supplies as promised despite its record of discrimination.
"We have to respect Myanmar's sovereignty," said Razali Ramli, from the 1Putera Club Malaysia, which helped organize the shipment along with a coalition of non-government organizations. "We hand over the aid in good faith."
The Rohingya have long faced official and social persecution in Myanmar, a majority-Buddhist country. Most do not have citizenship and are regarded as illegal immigrants from Bangladesh, even when their families have lived in Myanmar's Rakhine state for generations.
The conflict has been simmering for years but there are worrying signs that it is escalating into an armed insurgency, according to a recent report by the International Crisis Group.
The army launched its most recent crackdown in October following attacks on guard posts near the Bangladesh border that killed nine police officers. According to ICG, the border attacks were coordinated by a new insurgent group calling itself Harakah al-Yaqin, or the Faith Movement.
Organized by a network of Rohingya in Saudi Arabia and bankrolled by wealthy donors, the militant group is drawing Muslims disillusioned and desperate from years of disenfranchisement by the Myanmar government, the report said.
The government has denied abuses and has blocked independent journalists and aid workers from visiting the military's operation zone in Rakhine. On Wednesday, the country's leader, Aung San Suu Kyi, said a government-appointed commission on Rakhine will investigate some of the recent accusations of abuse.
"Where there is clear evidence of abuses and violations, the government will take necessary measures," she said in a statement carried by the country's state-run newspaper.
When Malaysia first proposed the flotilla in December, Myanmar officials said they would turn it away. In January they said they'd permit the vessel, but that it had to dock in Yangon instead of Sittwe, the capital of Rakhine.
Malaysia, which has a Muslim majority, is an outspoken critic of Myanmar's treatment of the Rohingya. Last month, Malaysian Prime Minister Najib Razak slammed Myanmar for letting the abuses continue.
On Thursday, dozens of Buddhist monks protested outside the port where the aid ship arrived, denying that the ethnic group Rohingya even exists. Many in Myanmar refer to the Rohingya as Bengalis, suggesting they belong in Bangladesh.
"We can accept if the ship is coming to help the Bengalis and we are not trying to stop the donation," said Win Ko Ko Lat, the leader of Myanmar Buddhist Nationalists Network. "But we want them to know that there is no Rohingya in Myanmar. This is our campaign."
A detailed report released last week by the U.N.'s human rights agency alleging widespread killing and rape by Myanmar government security forces has intensified international concern about the Rohingyas' plight.
On Wednesday, Pope Francis appealed for prayers for the Rohingya ethnic minority.
"These are good people, peaceful people," Francis said. "They're not Christians, but they're good, our brothers and sisters. And they have been suffering for years. They've been tortured and killed, simply because they are continuing their traditions, their Muslim faith. Let us pray for them," he said.
AP writer Eileen Ng in Kuala Lumpur, Malaysia, contributed to this report.