Major General Paween Pongsirin headed the task force that made 155 arrests following the discovery of mass graves and secret jungle trafficking camps along the Thai Malaysia border earlier this year.
His unit has since been disbanded.
''We were only given five months,'' General Paween said. ''The job is not finished yet.''
Major General Paween believes more senior officers would have been arrested if his unit had not been broken up so quickly.
Among those arrested were five military officers, including an Army lieutenant general, four senior police and four Interior Ministry officials, with local politicians, including members of councils and mayors, and a Health Ministry nurse. Former police and former politicians were also arrested.
One Army officer and a Navy officer have yet to surrender to police.
Major General Paween was seconded from Region 8 to Region 9 for the human trafficking probe. He has a reputation for enforcing the law, and ignoring reputations.
In this week's annual round of reassignments for 239 senior police, Major General Paween was given the role of deputy commander of Yala province - one of three troubled deep south border provinces.
Yala is reputed to be the heartland of human trafficking in Thailand. When he conducted the trafficking arrests, Major General Paween was based in Surat Thani, a province further north.
He was shocked to be so obviously exposed to the people he had been trying to bring to justice.
''I could have been appointed to other provinces but my masters chose the deep south,'' he said. ''I have pointed out that this is not good governance. I am very concerned for my safety. What have I done wrong?''
A career police officer, Major General Paween, aged 57, has taken leave and is now contemplating resignation.
''Human trafficking saw Thailand dropped to Tier 3 - the lowest level - on the US State Department's Trafficking in Persons report,'' he said. ''Trafficking remains a problem, not just for Thailand but for the whole region.''
Phil Robertson, Deputy Director, Asia Division, Human Rights Watch, said today: "Thailand needs to ensure that actual investigations on the ground to combat trafficking match the rhetorical commitments made by Bangkok's leaders to make this campaign a top priority.
'''Clearly that includes making sure that officials who have worked hard to get to the bottom of these cases are valued, and that their efforts are rewarded when they successfully act to end impunity for these horrific crimes.''
Major General Paween previously led a secret investigation into the taxi ''mafia'' on Phuket that resulted in scores of arrests and was called in to take over the murder investigation following the finding of the bodies of British tourists Hannah Witheridge, 23, and David Miller, 24, on a beach at the holiday island of Koh Tao in September last year.