Major General Paween Pongsirin said the five-month police probe was wound up and his investigation unit disbanded with more arrests yet to be made and trafficking networks unbroken.
The main reason he quit today is because acceptance of his new appointment as deputy commander of Yala province in Thailand's Deep South would expose him to revenge by trafficking network members who are still free.
Scores of arrests have been made since May by Major General Paween's team - including Army and Navy Officers, police and powerful local politicians.
But Major General Paween said: ''We were only given five months. The job is not finished yet.''
He alleges there are still senior people in uniform who have not been brought to book for their roles in the trade in people that flourished for years through Thailand until May, when the mass graves of Rohingya and Bangladeshis were discovered in secret jungle camps along the Thai-Malaysia border.
Why Thailand's probe into human trafficking was wound up with the chief investigator insisting arrests still had to be made is a question the Prime Minister and other senior government officials are likely to be asked many times before US State Department officials consider whether to lift the country from Tier 3 of its Trafficking in Persons ranking, the lowest level, next year.
With the disbanding of the trafficking investigation unit, the pregnant wife of one key Rohingya witness against several important suspects has been left to fend for herself without any protection or aid.
Major General Paween said today that ending human trafficking in Thailand was made a priority by Prime Minister Prayuth Chan-o-cha: ''I worked hard for the benefit of the country and I arrested some military officers and their [alleged] networks.''
Yala is a province where Major General Paween knows traffickers are still free so he has decided to reject his new appointment and resign instead after a long career as a highly-regarded honest policeman.
''This is very sad but I have no choice,'' he said. ''My first priority is to protect my life and the lives of my family.''
For years, human trafficking of stateless Rohingya from Myanmar (Burma) and later neighboring Bangladeshis grew into a multi-billion baht industry through Thailand with very few arrests and huge amounts of money changing hands.
Onlookers fear that with so many senior people in the networks still free, the hideous process is likely to resume at any moment - but with greater effort going into covering it up.
Thailand's grassroots effort to educate local officials and stop human trafficking from now on has not been matched by a desire to expose and arrest all those in uniform who were previously part of the trade in people.
Phil Robertson, Deputy Director, Asia Division, Human Rights Watch, said: ''Thailand's serious human trafficking problem is further from being solved today with the loss of Major General Paween, who did an exemplary job in investigating the human trafficking gangs involved in perpetuating the misery of the Rohingya, and prosecuting anyone involved, no matter how high their rank or important their connections.
''Transferring efficient and highly committed police in a punitive way, and leaving witnesses unprotected is precisely the way that Thailand elites have historically allowed human rights related prosecutions to unravel.
''The US government and the international community need to be asking some hard questions about this case to those in charge of Thailand's anti-trafficking efforts.
''Will these prosecutions of influential persons in the Rohingya trafficking cases go the same way that so many other trafficking prosecutions have gone in the past - let the accused play for time, look the other way as witnesses are intimidated or bought off, and then throw hands up in the air and look blameless when the prosecution cases implode at the court, allowing traffickers to walk free?
''It's time for action to be taken now to make sure that doesn't happen.''
Major General Paween, a career-long police officer now aged 57, will leave the force in 30 days unless authorities rescind the Yala appointment or hasten his resignation.
Thousands more Rohingya are expected to take to the sea in search of sanctuary after tomorrow's national election in Myanmar.
Declaration of Interest
Puketwan journalists Alan Morison and Chutima Sidasathian have to wait until November 30 for the possibility of a court verdict appeal by the Phuket Prosecutor's office to end. On September 1 a judge dismissed all criminal defamation and computer crimes charges against the reporters.
The case was brought by the Royal Thai Navy over Rohingya trafficking allegations originally published by Reuters news agency.
WATCH 'Shallow Graves,' from Channel News Asia
How a good cop helped Thailand turned the tables on trafficking, a nightmare that may not yet be over.
WATCH Al Jazeera Investigates - Genocide Agenda
A frightening look at what's happening in Myanmar (Burma) where documents reveal a plan to exterminate all Rohingya.
WATCH the Dateline documentary on Phuketwan
The Dateline documentary team from SBS Australia shared the three-day trial of Alan Morison and Chutima Sidasathian with participants for a show full of revealing insights.
WATCH Journey into Hell, by Four Corners
From Burma through Thailand, an award-winning current affairs team traces official complicity in the brutal treatment of the Rohingya and Phuketwan's part in its exposure.
WATCH How Trafficking Works
Phuketwan Investigative reporter Chutima Sidasathian says of traficking in 2014: ''It's worse and worse, day by day. Nobody cares''.
LISTEN The Rohingya Solution
A tragedy almost beyond words has been unfolding in Thailand, where a human smuggling network is thriving with the full knowledge of some corrupt law enforcement officers. Alan Morison of Phuketwan talks to Australia's AM program.