The Malaysian Maritime Enforcement Agency (MMEA) said the boat, discovered off the island of Langkawi, was ferrying 36 adults and about 20 children.
The Buddhist-majority country has branded the Rohingya as illegal immigrants.
Canada needs to deepen its commitment to human rights on the ground, by protecting women and girls, Rae says.
"[MMEA] provided early aid such as food, water and medicine", said North Regional Director Adm. Rozali Mohammed Said. "They are going there to fill up the land vacated by the Rohingya who have left Burma [Myanmar]. We will continue to support the government's efforts to ensure a safe and dignified life for the displaced Rohingya families and host communities".
The boat had stopped at a Thai island to restock itself on Saturday.
The United Nations estimates that more than 670,000 people fled to Bangladesh after fighting broke out last August between Rohingya militants and Myanmar's security forces in the western state of Rakhine. At that time, members of the insurgent group Arakan Salvation Rohingya Army (ARSA) allegedly attacked Myanmar police and army posts, provoking a brutal military crackdown on the Rohingya minority concentrated in Myanmar's Rakhine state.
Fortify Rights said it had documented other boat arrivals of Rohingya refugees in Malaysia and Thailand this year.
A Bangladeshi security officer said that Myanmar had resettled thousands of Buddhists by using a resettlement scheme which offers food, homes and cash.
"However, until today there is no detection or signs of the boat's entry", Haji Rozali said.
When he was appointed, Rae said his task would be to try and hear from all sides of the violence and to gather facts to shape a plan for how Canada and other countries should work to end the violence that has now displaced half a million Rohingya into neighbouring Bangladesh, with numerous women who have fled reporting rape and sexual violence by security forces.
"This is not a problem that will go away on its own", Matthew Smith, CEO of Fortify Rights, said in a statement.
It had set sail from Rakhine state, the United Nations refugee agency said.
"The sea and river points that the human traffickers used four to five years ago have been closed and these have been under strict vigilance", he said. Thai authorities confirmed that they sent the boat back out to sea.
But the refugees have arrived to find cramped settlements and often squalid conditions in Cox's Bazar, where hundreds of thousands who fled previous waves of persecution are already living.
Many of those refugees are now residing in sprawling and overcrowded Bangladeshi camps that threaten to be inundated with heavy rains - potentially overwhelming sanitation facilities and leading to outbreaks of water-borne diseases - during the upcoming monsoon season, which begins in May.
The report also suggests the federal government could target more of Myanmar's military leaders under its new Magnitsky Act that seeks to isolate human rights abusers by freezing assets and blocking travel.