A statement from the IDF said Israeli aircraft were attacking "a series of Hamas targets and infrastructure facilities," including headquarters, training camps and weaponry storage warehouses.
Israeli Prime Minister Ehud Olmert called for patience.
"The operation in Gaza intends primarily to change the situation in the south part of our country. It may take some time, and all of us are prepared to carry the burden and the pains that are [an] inseparable part of this situation," he said at a news conference with Barak and Foreign Minister Tzipi Livni.
However, he said, Israel wants to avoid causing a "humanitarian disaster" in Gaza.
"The instructions that we have given to our forces are to refrain from inflicting injury and harm on the innocent," he said.