The ship, carrying 2,200 tonnes of supplies, was due to drop off 500 tonnes at Myanmars largest city, Yangon. Plans to deliver the remainder to Rakhine state, where the Rohingya are located, and across the border in Bangladesh, appeared blocked.
Najib has been an outspoken critic of the treatment of predominantly Buddhist Myanmars Muslim Rohingya minority, calling on the government to stop attacks.
The Myanmar government, led by Nobel Peace Prize winner Aung San Suu Kyi, has denied the accusations, saying many reports of violence against Rohingya are fabricated. It insists strife in Rakhine State, where many Rohingya live, is an internal matter.
"This is a historic moment ... a noble effort that shows that all the pain and suffering of Rohingya in Myanmar will not go ignored," Najib said in a speech at a port near the capital of mostly Muslim Malaysia.
"We hear their pain, those who have been raped, murdered and burned alive."
Myanmar security forces launched a crackdown in the north of Rakhine State, on the border with Bangladesh, in October after nine policemen were killed in attacks on border posts the government blamed on Rohingya supported by foreign militants.
At least 86 people have been killed and about 66,000 have fled into Bangladesh since then to escape what refugees, residents and human rights groups say have been abuses by Myanmar forces including summary executions and rape.
The aid shipment, bound for Myanmars biggest city and port of Yangon, has been organised by Malaysian Muslim groups, as well as domestic and foreign aid groups.
The ship is expected to arrive in Yangon on Feb. 9 where it will unload 500 tonnes of supplies, organisers said.
It had been due to head on to Teknaf port in Bangladesh, near where many refugees from Rakhine are camped.
However, Malaysias foreign ministry said in a statement later that Bangladesh had decided not to allow the ship to dock at Teknaf. No further details on the decision were given.
Foreign Minister Anifah Aman has appealed to Bangladeshs High Commissioner to Malaysia for the decision to be reversed, the statement said. The missions organisers could be not reached for comment, Reuters reported.
Myanmar has not allowed the ship to sail to Sittwe, the capital of Rakhine State, as organisers had hoped.
Myanmar has also insisted that the aid to be distributed equally to both Buddhist and Muslim communities.
"We are still hoping with all our hearts that they will eventually allow us to visit Sittwe and distribute the aid ourselves," said the mission chief, Abdul Azeez Abdul Rahim.
Malaysia has urged the Association of South East Asian Nations to coordinate aid and investigate alleged atrocities committed against the Rohingya, breaking the 10-nation groups long-standing tradition of non-interference in each others internal affairs.
Myanmar, in turn, has accused Malaysia of exploiting the crisis "to promote a certain political agenda".
Najib hosted a meeting of representatives from the Organisation of Islamic Cooperation to discuss the treatment of Rohingya in January and urged Islamic countries to act to end the "humanitarian tragedy", Bernama reported.
Malaysias top counter-terrorism official has said Myanmar faces a growing danger of attacks by foreign militants in support of Rohingya.
Rohingya have faced discrimination in Myanmar for generations. They are not classified as a distinct group under citizenship laws and are regarded instead as illegal immigrants from Bangladesh, entitled only to limited rights.
The recent violence in the north of Rakhine State is the most serious since communal clashes in 2012 in which hundreds of people were killed.