The announcement comes a day after US President Barack Obama called on Myanmar to end discrimination against its minority Rohingya Muslim population, as the once pariah nation is widely viewed as catalysing their mass exodus.
More than 3,500 hungry and bedraggled Rohingya, as well as Bangladeshi migrants escaping poverty, have arrived on Thai, Malaysian and Indonesian soil in recent weeks after a trafficking crackdown by Thailand threw long-worn people-smuggling routes into disarray.
Rights groups have long accused Thai officials of turning a blind eye to -- or even complicity in -- the trade of migrants through its southern provinces and into Malaysia, but until now no military personnel have been implicated.
A court on Sunday issued an arrest warrant for Lieutenant General Manas Kongpan for his involvement in human trafficking, according to Thai national police chief Somyot Poompanmoung.
"Police are confident in the evidence (against him)," Somyot told reporters in Bangkok, but declining to give further details of Manas' alleged role in a multi-million dollar smuggling network.
Buddhist Myanmar's treatment of the Rohingya has drawn international condemnation, with critics accusing authorities of driving the Muslim minority out of the country by denying most of them citizenship and restricting everything from travel to employment.
On Monday Obama threw his political weight behind calls for Myanmar to address its role in the migrant exodus in his latest comments on the plight of the ethnic group.
"The Rohingya have been discriminated against significantly, and that's part of the reason they're fleeing," Obama said in Washington at an event with young leaders from Southeast Asia.
He also said that ending this discrimination was essential if Myanmar, which will hold landmark elections later this year, wanted "to succeed" in its transition to democracy.
No protection for wrongdoers
The current migrant crisis was sparked by a Thai police crackdown on trafficking after the discovery of dozens of shallow graves in the country's south on May 1 in a remote migrant camp bordering Malaysia.
The find threw well-established trafficking routes into chaos with smugglers abandoning their human cargo in the Andaman Sea and Bay of Bengal -- an estimated 2,500 migrants are still believed to be stranded at sea.
Thailand's military suspect Manas, 58, was a long-serving army officer in Thailand's south, the focal area of the trafficking probe.
According to the Royal Thai Army website Manas was the commander of the upper south province of Chumpon in 2013, before taking a senior position in Songkhla, which borders Malaysia.
He was moved this year to the Royal Thai Army Headquarters in Bangkok to act as an adviser -- although it was not immediately clear in what capacity.
The army suspended Manas on Tuesday and launched an internal probe into the allegations after intially ruling out the possible involvement of the military in the migrant scandal.
The arrest warrant also raises awkward questions for junta chief Prayut Chan-O-Cha, who has repeatedly justified his coup last year as a much-needed antidote to graft that he says had flourished under a series of elected civilian governments.
When questioned about possible wider military involvement in trafficking following the allegations against Manas, Prayut said he was unaware of other cases.
"I don't know. I am not the investigator," he told reporters in Bangkok Tuesday, but added: "Wrong is wrong. Let justice take its course. I will not interfere."
Thai police have so far arrested 51 people over the scandal, including senior local officials, with warrants out for 33 others.
Rights groups say the real money was made in southern Thailand, where brokers held the human cargo in jungle camps or safe houses awaiting release payments of around $2,000 from relatives or friends, or sold them on in bulk to farms and businesses in Malaysia.
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