The group – among them five children – were found on Koh Dong island in the southern Satun province on Saturday, said Lt. Gen. Surachet Hakpan.
Each year, thousands of the mostly Muslim minority Rohingya people, heavily persecuted in Buddhist-majority Myanmar, risk their lives in monthslong expensive journeys to reach Malaysia over Thailand's seas.
Police said they had been charged with illegal entry and could face deportation to Myanmar following a court case.
"We are providing humanitarian assistance and will investigate whether they are victims of human trafficking or if they entered illegally," Surachet said.
The group appeared "starving and was likely to have had no food for three to five days", a police statement said.
Group members told officers their boat was among three vessels carrying 178 people that had left Myanmar and Bangladesh, having paid an agent around 5,000 ringgit ($1,300) for the journey.
The first two boats carrying 119 people were stopped and arrested by Malaysian authorities, according to the Thai police statement.
The boat's crew then decided to abandon those onboard on Koh Dong island – telling them that they had reached Malaysia, the group told officers.
The incident comes after the bodies of 14 Rohingya people, including children, were discovered washed up on a beach last month after they attempted to flee Myanmar.
Hundreds of thousands of Rohingya people fled a military crackdown in the nation in 2017, bringing with them harrowing stories of murder, rape and arson.
Those still in Myanmar are widely seen as interlopers from Bangladesh and are largely denied citizenship, many rights and access to healthcare and education.
Muslim-majority Malaysia is a key destination for Rohingya fleeing persecution in Myanmar or refugee camps in Bangladesh.
In 2019, a Thai boat captain was charged with smuggling 65 Rohingya people from Myanmar after their vessel was shipwrecked on an island off the coast of Satun province.
The same area was the hub of a multimillion-dollar trafficking route, which unraveled in 2015 after the discovery of mass graves of Rohingya and Bangladeshi migrants along the border with Malaysia.