There were reports that some people were trapped in cars underneath the plane's wreckage, aviation officials said.
It was unclear what caused Friday's crash, though weather may have been a factor as the runway was wet following rain from Tropical Storm Alma, which hit the region this week.
'Desperate' survivors
The plane left San Salvador, capital of El Salvador, at 8:30am local time carrying passengers mostly from Honduras, El Salvador and Costa Rica and was flying into Tegucigalpa's main Toncontin international airport.
The dead included the pilot, a passenger and a person on the ground whose car was hit by the plane, Associated Press news agency said.
One of those killed was Harry Brautigam, a Nicaraguan who headed the Central American Bank for Economic Integration, Manuel Zelaya, the Honduran president, said.
Many passengers said they considered themselves lucky to have survived.
"Suddenly we felt a big noise and we were all trying desperately to get out," Mario Castillo, one of the passengers, told local television.
"The worst injured were the people in business class."
More than 7,500 litres of fuel spilled out of the jet and authorities tried to clear away hundreds of onlookers as they hosed down cars trapped under one of the plane's engines.
"The aeroplane's fuel could cause an explosion, and that would be an even bigger tragedy," Ivan Mejia, a security ministry spokesman, said.
The airport has long faced complaints over safety because of its short runway, high altitude and because pilots have to make an unusually steep approach.