The remaining members of the group were minors too young to appear in court.
Al Jazeera correspondent Selina Downes, who was in court, said some of the men who could not walk alone because of their injuries had to be helped by other refugees.
'I was tortured'
Earlier speaking to Al Jazeera in hospital in Ranong, several of the men showed evidence of serious injuries they said were inflicted after their boat was intercepted by the Myanmar military as they tried to escape the country.
One man who gave his name as Sutamin said he was taken onto a military vessel, where soldiers wrapped a cloth around a wooden stick, doused it in kerosene, ignited it and held it to his skin.
The Rohingya are a Muslim ethnic group from the northern Rakhine state of western Myanmar, formerly known as Arakan state.
Their history dates to the early 7th century, when Arab Muslim traders settled in the area.
They are physically, linguistically and culturally similar to South Asians, especially Bengali people.
According to Amnesty International, they suffer from human rights violations under the Myanmar military government, and many have fled to neighbouring Bangladesh as a result.
The vast majority of them have effectively been denied Myanmar citizenship.
In 1978 an estimated 200,000 Rohingyas fled to Bangladesh.
Approximately 20,000 Rohingya are living in UN refugee camps in Bangladesh.
"I got beaten. Everybody got beaten," he said. "But not a normal beating - this was very hard. I was tortured."
He said the soldiers had also tied a noose around his neck and threatened to strangle him.
Thai medical teams treating the group said they were shocked at the extent of their wounds.
Human rights groups have condemned Thailand's handling of the Rohingya issue and urged the Association of South-East Asian Nations (Asean), the regional body which includes Thailand and Myanmar as members, to take urgent action.
"Taking victims to court is not going to solve the problem," Debby Stothard, of the Alternative Asean Network, told Al Jazeera.
"Addressing the problems of Burma is going to solve the problem."
Myanamar was formerly known as Burma.
She said Asean should abandon its policy of non-interference in members internal affairs and implement "a regionwide policy to deal with asylum seekers in a humane manner".
The Rohingyas are a stateless Muslim minority group who face persecution in Myanmar, whose military government does not recognise them as citizens.
Tens of thousands have fled the country, often in rickety wooden boats to Thailand from where they travel overland to Malaysia.
"There is no reasonable ground to believe that these migrants fled from their country of origin for well-founded fear of being persecuted"
Thai government statement
Earlier this month the Thai army was itself accused of abusing Rohingya migrants, beating them and forcing their boats to return to sea without food and fuel, or with their boat's engines disabled or removed.
Reports from survivors who washed up on India's Andaman islands and northwest Indonesia suggested hundreds who were towed out to sea by Thai soldiers may have died.
Human rights groups say the Thai military has been engaged in a secret and systematic campaign against the Rohingya, because of suspicions they may be involved with Muslim separatist fighters in Thailand's south.
The Thai military and government have rejected the allegations.
They also deny that the Rohingya face persecution in their country of origin.
On Wednesday the Thai government issued a statement reiterating its position that the Rohingya are illegal economic migrants, not refugees, and will never be let into the country.
"There is no reasonable ground to believe that these migrants fled from their country of origin for well-founded fear of being persecuted," the statement said.
Larry Jagan, a Myanmar specialist, told Al Jazeera that the root of the problem lay with the government in Myanmar, and any solution would require a strong international approach.
He said the repression carried out in Arakan, the region of Myanmar where most Rohingya come from, was "immense".
"It's much worse than abuses committed by the government elsewhere in the country, but it's not new - this has been going on for about 20 years."