Flight details provided by Captain Danai Chumapai contradict reports that wounded bomber Seadi Morati, 28, arrived in Thailand on a flight from South Korea via Phuket.
A third suspect is believed to have escaped to Malaysia after yesterday's explosions in Bangkok exposed a suspected bomb plot, possibly aimed at Israeli diplomats.
Morati, who lost both legs as a result of the blasts in Bangkok yesterday, arrived on Phuket last Wednesday on AirAsia Flight AK 826 and cleared Immigration at 1.37pm, according to Captain Danai.
Travelling with him was a second Iranian, Mohammad Khazaei, 32. The two men arrived as normal passengers on the scheduled flight and nothing special was noted about them, the captain said.
The two men were recorded by Phuket Immigration as boarding Bangkok Airways Flight PG 274 at 4pm to Bangkok on the same day.
The short period between the mens' arrival on the flight from Kuala Lumpur to Phuket and their departure on the flight from Phuket to Bangkok probably means they stayed at Phuket International Airport between trips.
Captain Danai said that the data recorded at Phuket International shows that Mohammad Khazaei had previously flown to Thailand, entering via Bangkok's Suvarnabhumi International Airport, in December.
Details of the pair's flight from Malaysia via Phuket are likely to intensify inquiries in the Malaysian capital.
Officials are concerned to deflect damage to the tourism industry on Phuket and in Thailand as about 10 nations, including Britain and the US, reacted to the Bangkok blasts by issuing travel alerts.