A Malaysian ship carrying 2,300 tonnes of aid for tens of thousands of persecuted Rohingya Muslims arrived in Yangon where it was met by Buddhist protesters.

Health workers and activists crowded onto the deck of the Nautical Aliya as it docked at Thilawa port near Myanmar's commercial capital on Thursday carrying food, medical aid, and clothing.

Organisers of the aid shipment said 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 organise the shipment along with a coalition of non-government organisations. "We hand over the aid in good faith."

Myanmar's social welfare minister was among a delegation meeting the ship, which has been at the centre of a rare diplomatic spat with fellow ASEAN member Malaysia.

Outside the docking area, dozens of Buddhist monks and demonstrators waited waving national flags and signs reading: "No Rohingya".

READ MORE: 'Hundreds of Rohingyas' killed in Myanmar crackdown

"We want to let them know that we have no Rohingya here," a Buddhist monk named Thuseitta, from the Yangon chapter of the Patriotic Myanmar Monks Union, told AFP news agency.

Myanmar denies citizenship to the million-strong Rohingya, despite many of them living on its soil for generations.

Buddhist nationalist groups are especially strong in their vitriol, rejecting Rohingya as illegal immigrants from neighbouring Bangladesh.

Hundreds of Rohingya have reportedly been killed in a brutal campaign launched by security forces in October, which the United Nations says may amount to ethnic cleansing.

The violence started after a series of attacks by armed men on border posts killed nine policemen.

Tens of thousands of Rohingya have fled to neighbouring Bangladesh, bringing harrowing tales of murder and sexual assault.

"We've documented atrocities, serious crimes that have been committed by Myanmar's security forces," Matthew Smith, executive director of the group Fortify Rights, told Al Jazeera.

"We're documenting killings, we're documenting mass rape … throats being slit, bodies being thrown into fires, villages burned to the ground."

Myanmar's treatment of the Rohingya has sparked criticism from Muslim-majority Malaysia in a rare spat between the Southeast Asian neighbours.

Myanmar initially refused to allow the aid ship into its waters and has barred it from sailing to Rakhine's state capital, Sittwe.

READ MORE: UN - Rohingya may be victims of crimes against humanity

Al Jazeera's Yaara Bou Melhem, reporting from Yangon, said the aid will be unloaded and distributed by the government from there.

"What we know is that a plane from here in Yangon will take the aid to Sittwe, which is nearest to the conflict zone ... to distribute the aid among both Rohingya and Buddists," she said.

"There's no clear indication the aid will reach the Rohingya, because the area has been in lockdown since the renewed fighting began in October."

The delivery comes days after a blistering report from the UN accused Myanmar's security forces of carrying out a campaign of rape, torture, and mass killings against the Rohingya.

Based on interviews with hundreds of escapees in Bangladesh, investigators said the military's "calculated policy of terror" was likely to have amounted to ethnic cleansing.

For months, Myanmar has dismissed similar testimonies gathered by foreign media and rights groups as "fake news" and curtailed access to the region.