Passengers on a nearby flight waiting to depart watched in horror as flames shot out and a dark plume of smoke billowed from the wreckage, witness Ben Cundall told CNN.
"Everyone was screaming," he said. "The flames were the length of an aircraft, so it was clear to everyone what had happened straight away."
The Fairchild Metroliner, which was taking part in an operation to track illicit human and drug trafficking routes, crashed at 7:20 a.m. (1:20 a.m. ET) Monday, officials said.
"Official information, footage and eyewitnesses, including three members of the Armed Forces of Malta at the nearby Safi Barracks, and two commercial airline pilots, clearly indicate that there was no explosion prior to impact," the Maltese government said in a statement
. "Several inquiries, as established by international rules and the laws of Malta, are currently underway to establish all facts."
All five people aboard the plane were French nationals, the statement said.
Witness Lauren Azzopardi, who filmed the crash on his car's dash cam as he was driving to work, told CNN he heard a blast as the plane slammed into the ground.
"I saw the plane go vertical. It was coming at a very fast speed," Azzopardi said. "It kind of turned and planted into the ground."
The flight was part of a French customs operation that had been going on for the past five months, Maltese officials said in statement.
It had been scheduled as a local flight and was due to return within hours "without landing in third countries," the statement said.
The plane was registered in the United States to a company called Worldwide Aircraft Services. The Maltese government said it had been leased to a Luxembourg company.
Earlier reports indicated that EU border officials were on board the plane, but EU Foreign Affairs Chief Federica Mogherini said on Twitter that no EU officials were involved in the crash.