The tunnel belonged to Palestinian Islamist movement Hamas and was intended for attacks as opposed to smuggling, according to Israeli military spokesman Jonathan Conricus.
Since October, the army has demolished three terror tunnels - one in October, one in December and this latest one, which penetrated Egypt and reached underneath the Kerem Shalom border crossing. There were no reports of injuries in the destruction of the tunnel.
The military said that it has no intention to further escalate the situation but will "continue to act against any violation of Israeli sovereignty".
The IDF destroyed the tunnel on Saturday night, describing its running under the border crossing as both "cynical" and "absurd". Most tunnels that run from Gaza to Egypt are used to smuggle goods into the economically starved territory.
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"We are happy to be able to have those capabilities", Conricus said. The IDF said it holds Hamas responsible for all activity emanating from Gaza.
Nezar Ayyash, the head of Gaza fishermen union, earlier said the fisherman had been shot by gunfire from the Egyptian border.
Lt Col Conricus said forces had been monitoring its construction for some time and an imminent attack on Israelis was possible.
He said Israeli jets struck part of the tunnel and a new set of sophisticated "tools" destroyed the rest.
The strike came shortly after the military announced it would not be opening the Kerem Shalom Crossing into the Gaza Strip on Sunday, following a "situational assessment".
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