Humanitarian mission vessel, Nautical Aliya arrived after 12 days today, at Chittagong Port in Bangladesh about 12.30pm local time.
Thousands of Rohingya have fled alleged human rights abuses in Myanmar, with many running to neighbouring countries.
The coordinated attacks on three border posts on October 9, which killed nine policemen, prompted the Myanmar government to launch a brutal crackdown on Rohingya Muslims.
Almost 69,000 Rohingyas have fled across the border to Bangladesh since Myanmar began a military crackdown in Rakhine state after a series of militant attacks killed 9 policemen on Oct 9.
Myanmar's government has pledged to investigate the allegations after spending months dismissing similar reports from global media and rights groups as "fake news".
He added that 25 people from the ship have been allowed to get off onto land, and that this group will make its way to the Kutupalong refugee camp near Cox's Bazar.
A port official in Chittagong said a ceremony would be held on Tuesday with a senior foreign ministry official and Malaysia's ambassador in attending to receive the shipment. According to a 2015 UNHCR factsheet, at least 32,000 registered and 200,000-500,000 unregistered/undocumented Rohingya are living in Bangladesh, mostly in Cox's Bazar.
The aid will go to Teknaf, Cox's Bazar, where the Rohingya camps are based, for distribution.
The Rohingya Muslims are being butchered there unceasingly by the Buddhist people and the government of Myanmar ruled by a Nobel Peace laureate, Aung San Kyi.
Buddhist nationalist groups are especially strong in their vitriol, rejecting them as illegal immigrants from Bangladesh.
The Food Flotilla for Myanmar is organised by the Putra 1Malaysia Club and the Malaysian Consultative Council for Islamic Organisations with the participation of 182 volunteers from Malaysia and other countries.
About 1.1 million Rohingya live in apartheid-like conditions in northwestern Myanmar.
Hundreds of thousands of Rohingya are camping in Teknaf officially and in unregistered camps.