Capt. Somkiat Ponprayun says the Explosive Ordnance Disposal unit believed they had defused the device, which was found Monday along a road in Bacho district in Narathiwat province.
He says officers also found a banner with a message against ongoing peace talks between the government and the insurgents.
Somkiat said the marines took the bomb to their base to study it, and it then exploded. He said it may have had a second triggering device.
Four marines were killed and six others were injured in the blast.
More than 5,000 people have been killed in Thailand's three southernmost provinces since an Islamist insurgency erupted in 2004.
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