Since carrying out a nuclear test in May, North Korea has been under UN sanctions aimed at cutting off its arms sales which are thought to net Pyonyang more than $1bn a year.
The North's biggest arms sales come from ballistic missiles and its customers include Iran and other Middle Eastern states, according to US government officials.
Mercedes Stephenson, a defence and security analyst based in Toronto, told Al Jazeera the incident was "tangible proof that North Korea is actually engaging in this activity".
"It's significant in that they've actually caught this particular shipment, [but] it's small in the overall amount of shipping that we suspect North Korea is actually doing ... it is very difficult to track illicit arms shipments."
Media reports said that Thai authorities were alerted about the aircraft's cargo by US officials.
Wattanayagorn did not comment on the reports but said: "We have been working with many agencies from many countries and we will continue to do so."
He said the aircraft had been due to stop again for refuelling in Colombo, Sri Lanka, but that it was unclear what the crew's ultimate destination had been.
Thai police said that four of the five men arrested are from Kazakhstan and one is from Belarus.
The men denied charges of arms possession and were refused bail.