Rafah residents began to flee their homes in panic as the aircraft struck three times before dawn, Hamas officials said. There was no initial word of any casualties.
An Israeli army spokeswoman said she was checking the report.
The strike came as an apparent revange to Tuesday's attack by Gaza militants on an Israeli military vehicle that was hit by a roadside bomb while patrolling the Gaza border, killing one soldier and wounding three others.
An air strike shortly afterwards killed one Palestinian on a motorcycle but Israeli Prime Minister Ehud Olmert said late on Tuesday that it was only an initial reaction and that Israel's full response was still to come, Israeli media websites reported.
In addition, a Palestinian man, apparently a farmer, was killed in exchanges of fire between IDF troops and Palestinians in Gaza after the bomb was detonated, according to Palestinian reports.
Israel began its attack on Gaza, ruled by the Islamist group Hamas, on Dec. 27 saying it wanted to stop militant rocket fire into nearby Israeli towns. It ended with some 1,300 Palestinians and 13 Israelis were killed.
Hamas and Israel declared separate ceasefires and are negotiating through Egyptian mediators on a longer-term truce. Hamas wants Israel to lift its blockade of the Gaza Strip.
Israel wants guarantees that Hamas will not again fire rockets at Israeli towns.
Source: Reuters