In recent weeks more than 3,500 Rohingya Muslims, a persecuted minority in Myanmar, and Bangladeshi economic migrants have arrived on Thai, Malaysian and Indonesian soil, prompting a regional migration crisis.
Rights groups have long accused officials in junta-ruled Thailand of turning a blind eye to human trafficking, or even complicity in the trade - but until now no army official has been implicated.
"Police are confident in the evidence," Somyot told reporters ahead of a press conference about Thailand's anti-trafficking operations at police headquarters in Bangkok.
"I am confident he will not flee," he said, adding that police had not yet contacted the military about handing Manas over to them.
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Manas is aged 58, according to a court document published in Thai media. No further details of his alleged involvement in the trade were immediately available from Somyot.
Prayut has repeatedly justified his power grab as a necessary evil to excise widespread graft he says had flourished under a series of elected civilian governments.
He has also said the tens of thousands of migrants who make the sea journey south each year are aiming for Malaysia, rather than Thailand.
An estimated 2,500 migrants are still believed to be stranded at sea after a recent Thai police crackdown on trafficking threw well-worn regional routes into chaos with smugglers abandoning their human cargo in the Andaman Sea and Bay of Bengal.
In January, months before the current crisis unfurled, Thailand said more than a dozen government officials - including senior policemen and a navy officer - were being prosecuted for involvement or complicity in human trafficking.