"You can see all manner of discarded items including shoes, caps, blankets, water bottles ... No one here knows what has happened to these 46 people, or at least no one is telling us," Downes said.
The allegations were made as Thailand offered to host a regional conference aimed at stemming the flow of illegal immigrants from Myanmar and Bangladesh.
Thousands of Rohingya and Bangladeshis leave Myanmar aboard rickety boats each year in hopes of finding work elsewhere, with many travelling to Thailand by sea and then overland to Malaysia.
Saman Maneejansuk, a member of a civilian force trained by Thailand's military to round up illegal immigrants, told Al Jazeera that the Rohingya were a threat to the area's security.
"We practise how to shoot guns and train after dark because sometimes the Rohingya come at night by boat and run up into the hills. We don't want them coming here," he said.
The alleged abuse of boat people by Thai soldiers came to light after accounts emerged of a group of Rohingya who were reportedly beaten before being towed back out to sea after being intercepted off Indonesia.
Reports from survivors who washed up on India's Andaman islands and northwest Indonesia suggested as many as 550 of the 992 towed out to sea by Thai soldiers were dead.
Abhisit Vejjajiva, Thailand's prime minister, said that the allegations were being investigated.
"The reported or alleged incidents that took place is something that the armed forces will now look into to check," he said.
"They have also made it clear that if any of the officers are involved in such violations they would be held accountable."
Benjamin Zawacki, a researcher for Amnesty International, said that the regional conference could help the Rohingya and other migrants that feel their only option is to attempt the perilous journey to Malaysia.
|It was unclear what had happened to those onboard dozens of boats abandoned in Thailand
"A solution needs to be found to this, and it needs to be a sustainable solution, and the only way that can happen is if this issue is dealt with regionally," he said.
Thai foreign ministry officials met envoys from India, Indonesia, Bangladesh, Malaysia and Myanmar on Saturday to discuss the exodus of refugees from camps in Bangladesh, Thani Thongpakdee, a ministry spokesman, said.
"We are also in talks with the UN High Commissioner for Refugees both in Thailand and in Geneva to help alleviate what these people are facing right now," he said.
Myanmar refuses to recognise the Muslim Rohingya minority in western North Rakhine state as a distinct ethnic group.
Human rights activists say they havee abused and exploited, forcing many to flee abroad, mainly across the border to Bangladesh.
"They are literally disenfranchised, the government of Myanmar does not see them as citizens of the country," Zawacki said.