Health workers and activists crowded onto the deck of the Nautical Aliya as it docked at Thilawa port.
Health workers and activists crowded onto the deck of the Nautical Aliya as it docked at Thilawa port near Myanmar's commercial capital carrying food, medical aid and clothing.
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."
"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 at the docks.
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 them as illegal immigrants from Bangladesh.
Hundreds of Rohingya are thought to have been killed in a brutal campaign launched by security forces in October, which the United Nations says may amount to ethnic cleansing.
Tens of thousands have fled to neighbouring Bangladesh, bringing harrowing tales of murder and rape.
Myanmar's treatment of the Rohingya has sparked criticism from Muslim-majority Malaysia, in a rare spat between Southeast Asian neighbours.
Myanmar initially refused to allow the ship into its waters and has barred it from sailing to Rakhine's state capital Sittwe.
Part of the aid will instead be unloaded in Yangon and transported overland to the north of Rakhine state, site of the military crackdown.
The rest will be taken to Teknaf port in southern Bangladesh, where almost 70,000 Rohingya have fled since October to escape the violence.
The government has also demanded that the aid be distributed to both Rohingya and Buddhist ethnic Rakhines.
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" very likely amounted to ethnic cleansing.
For months Myanmar has dismissed similar testimony gathered by foreign media and rights groups as "fake news" and curtailed access to the region.
The UN's top official on preventing genocide, Adama Dieng, said this week that a government commission tasked with investigating allegations of abuse was "not a credible option".
Critics have rejected the state-appointed body, which is led by retired general and Vice President Myint Swe and includes no Muslims, as toothless and biased.
In a meeting on Wednesday Myint Swe admitted that "among the facts and accusations included in the (UN) report, there may be something special to be investigated," state media reported.