Smoke was billowing from the bright yellow plane of German logistics giant DHL as it ground to a halt, having slid off the runway when it spun and broke up around the rear wheels.
Two crew members aboard were "in a good condition," said the chief of Costa Rica's firefighters, Hector Chaves.
Nonetheless, the Guatemalan pair were sent to hospital as a precaution "for a medical check-up," according to Guido Vasquez, a Red Cross worker.
The pilot was shaken up but both crew were conscious and "remember everything vividly," added Vasquez.
The accident happened just before 10:30 am (1630 GMT) after the Boeing-757 plane, which had taken off from the Juan Santamaria international airport outside San Jose, was forced to return 25 minutes later for an emergency landing due to a mechanical failure.
The crew apparently had alerted local authorities to a hydraulic problem.
The airport was closed until 6:00 pm.
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