A senior Thai policeman who headed an investigation into human trafficking for the country's military government has fled Thailand in fear of his life and is now requesting political asylum in Australia.

Police Major General Paween Pongsirin had been investigating the trafficking of Muslim Rohingya migrants after the discovery of mass graves and 26 corpses in southern Thailand in early May.

The bodies are believed to be those of Rohingya refugees and were victims of the traffickers.

Major General Paween claims his investigation was stopped by highly influential people within the government, the military and the police.

He said high-ranking government officials repeatedly obstructed the investigation.

"A lot of government officials should be facing justice," Major General Paween told 7.30.

"There are good soldiers but the police and the military are involved in running the human trafficking.

"Unfortunately the bad police and the bad military are the ones that have power."

The investigation has now been halted.

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Major General Paween's inquiries have led to arrest warrants being issued for 153 people, including numerous local politicians, wealthy businessmen, four policemen, members of the Thai army, navy, police and the Internal Security Operation Command.

Ninety-one people have been charged and have begun appearing at trials in the capital, Bangkok.

One of the suspects was former senior army advisor Lieutenant General Manas Kongpan.

Major General Paween said the trials were now compromised.

"How can the witnesses believe that they will be protected for any period now?" he said.

And he believes the police have lost their nerve to prosecute the cases properly.

"I think the people there now will not be brave enough to continue," he said.

'Now I realise how dangerous it was'

Human Rights Watch Asia deputy director Phil Robertson said Major General Paween was the right man for the job.

"This is a person who investigates based on the facts on the ground and the evidence and follows the leads wherever they may go," he told 7.30

"So if they thought they were bringing someone in to give initial credibility to the investigation, then he would be deterred or pushed off from following the leads to their logical conclusion, I think they picked the wrong man."

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Mr Robertson said he was also worried about Major General Paween's future.

"He was brought in as a hard-nosed, experienced investigator — someone who has a reputation for being forthright in being incorruptible," he said.

"And what [he] found was so explosive that he feels it is no longer safe for him to remain in Thailand."

At the beginning of November, Major General Paween was told he was being transferred to the south of Thailand, where many of the suspects he is pursuing live and have influence.

But he formally resigned before being transferred, citing serious concerns for his security.

He now fears for his life.

"I had to do just my duty [and] not to think of dangers or trouble, but now I realise how dangerous it was," Major General Paween said.

Major General Paween is now looking for a safe haven.

"I worked in the trafficking area to help human beings who were in trouble," he said.

"I wasn't thinking of a personal benefit but now it is me who is in trouble. I believe there should be some safe place for me, somewhere on this earth to help me."