Such tunnels have been used to carry out attacks in the past.
Residents in Gaza said Israeli jets bombed an area east of the southern town of Rafah, by the Egyptian and Israeli borders, late on Saturday night.
But Lt Col Conricus said this did not mark "more of the same" since it involved the most advanced technological means Israel has deployed.
"There are those who have said the IDF just targeted sand dunes - this is incorrect", Netanyahu said in remarks to Israeli media before departing on his trip to India.
The army said that the tunnel, which ran for nearly a mile, extended 650 feet into Israeli territory, and was used to bring weapons into Israel for use by terrorists. The Israeli military has invested heavily into developing new technologies and intelligence-gathering capabilities to uncover and neutralize tunnels from Gaza and is in the process of building an underground barrier spanning the entire border with the Hamas-run enclave.
"The terrorist organization Hamas is responsible for everything happening in and out of the Gaza Strip", an IDF statement said. "Hamas needs to understand that we will not allow the continuation of these attacks and we with even greater force".
The tunnel was positioned in southern Gaza, near the Kerem Shalom crossing where the borders of Israel, Gaza and Sinai meet.
Defence minister Avigdor Lieberman said the tunnel's construction was a clear violation of Israeli sovereignty and destroying it delivered a stinging blow to one of Hamas' most significant assets.
The Israeli military said it has destroyed three tunnels in the past two months.
He said he was not aware of any casualties from the destruction of the tunnel, which was still being built.
The attacks from Gaza, which Israel has blamed on groups not affiliated with Hamas, have drawn Israeli air strikes, usually on targets that have been evacuated.
Israel shut down the crossing on December 14 following multiple rockets and mortar attacks from Gaza, along with Erez Crossing, through which people enter and exit the Strip.