Palestinian gunmen used tunnels to blindside Israeli forces during a 2014 Gaza war. Israel has since been developing detection technologies and constructed an underground concrete barrier with sensors to foil attempts to dig across the border.
The military has exposed several tunnels in recent years.
The latest tunnel had been "neutralised" a year ago but was being restored with two routes that led toward Israel, though they did not pass the underground barrier, a military statement said.
Hamas spokesman Fawzi Barhoum said the group had "the right to use all means to reinforce and develop its capabilities" and that the Israeli announcement presented "false achievements" to the public.
The announcement came about a week after a flare-up in cross-border violence, during which Israeli forces bombarded Palestinian targets and Islamic Jihad militants fired hundreds of rockets towards Israel.
Israel focused its three-day operation on Islamic Jihad, an Iranian-backed militant group, while avoiding a direct confrontation with the larger and more powerful Hamas that has governed coastal Gaza since 2007.
"We were aware of this tunnel but we waited for this (operation) to be over before we acted," an Israeli military spokesman told Reuters.
He said it was a "non-kinetic operation," meaning Israel flooded the tunnel, which ran deep underground.
It was a "pretty advanced tunnel" which would have been intended to move gunmen or fighters into Israel to attack Israelis, the spokesman said.
(Reporting by James Mackenzie, Nidal al-Mughrabi and Ari Rabinovitch, editing by Mark Heinrich)