Israeli warplanes bombed the northern and southern Gaza Strip early Friday, the military said, DPA reported.
No immediate injuries were reported.
A military spokesman in Tel Aviv said the targets were underground tunnels dug by militants for infiltrating Israel and carrying out attacks against soldiers or civilians near the border.
Two such tunnels were destroyed east of the southern Gaza Strip town of Khan Younis, where fire spread in a field according to witnesses.
The third tunnel was near the northern Gaza Strip town of Beit Hanoun, at what was said to be a training site of the radical Islamist Hamas movement ruling Gaza.
The tunnels were dug about one kilometer from a security fence along Gaza's border with Israel, said the spokesman.
He said the attacks were retaliation for a rocket fired from Gaza at southern Israel late Thursday which followed one on Wednesday.
Palestinian militants fired about 50 rockets and mortar shells at Israeli territory since the beginning of the year, despite relative calm since Israel ended a deadly and devastating, three-week offensive in Gaza in the winter of 2008-2009.
Some 1,400 Palestinians were killed in that offensive, as were 13 Israelis, launched to curb the rocket and mortar fire from the strip.
"The IDF (Israel Defence Forces) remains committed to protecting the citizens of Israel and will continue to act against terror. The IDF holds Hamas solely responsible for terror emanating from the Gaza Strip," said a statement issued by the military.