Seven tanks and armoured bulldozers, backed by helicopter gunships moved into the area between Rafah and the town of Khan Yunis on Monday, witnesses said.
Aljazeera's correspondent reports that the occupation army has closed off all roads linking the two towns.
Unlike other invasions, the correspondent added, Monday's raid began from the northern and eastern parts of Rafah, in an attempt to completely isolate it from the rest of Gaza. The tanks and bulldozers destroyed everything in its way, including water pipes, the correspondent said. A curfew has also been imposed on the town.
Bulldozers piled sand embankments across the main road and a tank fired three shells at an empty Palestinian police post on the road, Palestinian security officials said.
Witnesses also reported large forces massing on the outskirts of the town.
Israeli military sources confirmed the target of the operation was to isolate Rafah in an attempt to search for Palestinian activists and weapons, the correspondent said.
Another report said the army said the move was aimed at preventing what it called "militants" moving between the two towns.
Rafah has been the scene of devastating raids over the past few days, with the army demolishing up to 100 Palestinian homes. Up to 1000 Palestinians have been left homeless, as a result of the demolitions. Seven Israelis soldiers were also killed in the town along the border with Egypt.