Two Rohingya men died on Monday night in detention in Nakhon Si Thammarat province.
They were arrested on Sunday along with 96 other Rohingya at a checkpoint in Hua Sai district.
The latest deaths take the toll to three after a woman was declared dead from suffocation on Sunday.
She is believed to have been killed by cramped conditions in the pickup truck she was travelling in.
According to police, one of the men died from diarrhoea at the local hospital. The other had a blood infection and died in transit.
Both men were buried yesterday at the Thai-Muslim cemetery in Hua Sai.
Police and local authorities are currently overseeing and communicating with the Rohingya through interpreters.
They have divided the migrants into two categories: those who intended to make the journey to Thailand and those who were deceived into doing so by human traffickers.
Some of the Rohingya said they had paid agents to take a boat to Malaysia to meet their families there.
Others said family members had been killed and their houses in Rakhine State burnt down before they were forced onto boats.
Two drivers of the vehicles that transported the migrants were charged with breaching the Human Trafficking Suppression and Prevention Act, said Pol Maj Somchai Auam-thanom, deputy commander of Provincial Police Region 8.
The suspects, Sawat Phadungchart, 29, from Ranong and Suthipong Chuaypat, 49, from Surat Thani, were arrested at the scene. Three drivers escaped.
Police have evidence pointing to a key figure behind the human trafficking ring, Pol Maj Somchai said.
Investigators found the convoy of migrants originally had 400 Rohingya, meaning 302 are still at large.