Defence Minister Avigdor Lieberman said it was the longest and deepest tunnel of its kind Israel had discovered.
A military spokesman said it had been dug since the 2014 Gaza war, when Israel destroyed more than 30 tunnels which it said were meant for attacks.
Israel is using sophisticated measures to thwart tunnels dug by militants.
Military spokesman Lt Col Jonathan Conricus said the tunnel had been dug by Hamas and began in the area of Jabaliya in the northern Gaza Strip. He said it penetrated several metres into Israel in the direction of Nahal Oz, but did not yet have an exit.
The tunnel stretched "several kilometres" into Gaza and connected with other tunnels from which attacks could be launched, he said.
Israel disabled the tunnel over the weekend, according to the military. "We filled the tunnel with material that renders it useless for a very long period of time," Col Conricus said.
It was the fifth Gaza tunnel to be destroyed by the Israeli military in recent months, Col Conricus said.
Some of the tunnels have been built by Palestinian militant group Islamic Jihad and others by Hamas, the Islamist group which controls Gaza.
Since last year, Israel has been using special equipment to detect the presence of tunnels, and is building a hi-tech barrier above and below ground along its border with Gaza to prevent new tunnels being dug.
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