The officials say the missiles hit a rugged and remote area on the edge of the Lebanese border town of Arsal on Monday. There were no immediate reports of casualties.
In recent months there have been clashes on the Syrian side of the frontier in the area between rebels and Syrian troops.
Lebanese forces have in the past detained people caught trying to smuggle weapons into Syria from Lebanon in the region.
Syrian shells have hit Lebanese territory in the past but the air raid appears to be the most serious violation since Syria's crisis began in March last year.