It is believed the commander allegedly turned a blind eye and seldom intercepted vessels containing boatpeople - then allegedly claimed money from those who did intercept the boatpeople to hand them to traffickers.
Charges laid against Commander Kampanart Sangtonggeen and three Army captains only enlarge the scale of the alleged trafficking off Thailand's coast by officials wearing several different types of uniforms.
The Prime Minister of Thailand, Prayuth Chan-o-cha, and the Commander in Chief of the Army, Udomdej Sitabutr, have called for full investigations of all human trafficking issues.
Phuketwan believes all senior officers who have held positions along the coast and in the south over the past five years should now voluntarily open their bank accounts to the scrutiny of investigators.
As the recent victims of false claims of criminal defamation and computer crimes made by one or two misguided officers misusing the good name of the Royal Thai Navy, Phuketwan journalists Alan Morison and Chutima Sidasathian believe the opening of bank accounts to scrutiny is the only way innocent officers can be completely cleared.
''The network of corruption involving boatpeople has involved many billions of baht,'' Morison said today. ''The way for Thailand to now clear its name is to open the bank books of everyone involved to establish their innocence.
''This is something that all good officers should be prepared to do, voluntarily.''
A Phuket Provincial Court judge dismissed all charges of criminal defamation and Computer Crimes Act counts against Morison, Khun Chutima, and Phuketwan's business parent, Big Island Media, on September 1. The Royal Thai Navy has 30 days in which to appeal.
The charges concerned a 41-word paragraph reproduced on July 17, 2013, on Phuketwan directly quoting a Reuters news agency paragraph, word for word. Reuters was not charged and failed to act in defence of the paragraph written by its journalists.
The paragraph was contained in a series on the Rohingya boatpeople that won a Pulitzer Prize in 2014.
Commander Kampanart, while a member of Royal Thai Navy 3, led patrols along the 600 kilometres of Thailand's Andaman coast, a popular destination for many years for Rohingya traffickers' vessels from Myanmar (Burma). Navy statistics show very few of these vessels were apprehended.
Those that were met by Navy ships were usually ''helped on'' to a third country and given food, water and other aid on the promise that they would not land in Thailand.
The three Army officers named over human trafficking charges at the weekend are Colonel Nattasit Maksuwan, Captain Wisut Boonnark and Captain Santad Peatnoi. Major General Manas Kongpan is also being held without bail on human trafficking charges.
Morison, an Australian, says fighting the law suit by the Royal Thai Navy cost him $60,000 to $100,000 in lost income. Phuketwan is due to close on January 1.