Palestinian media reports said that the target was a cross-border smuggling tunnel operated by Hamas.
"Hamas must understand that we will not permit these attacks and we will respond with even greater force", Netanyahu said in remarks to Israeli media before departing on his trip to India.
It was also noted that Kerem Shalom border crossing on the Gaza Strip-Israel border would be closed later in the day for security reasons.
The strikes occurred within the Gaza Strip, while further means were used in Israeli territory.
Conricus said the tunnel destroyed Saturday was dug by key operatives of Hamas and was 1.5 km long (about one mile), penetrating 180 kilometres under the Kerem Shalom border crossing into Israel and into Egypt.
Israel's operation on Saturday was conducted against a backdrop of a number of rocket attacks against Israel, emanating from the Gaza Strip.
The tunnel stretched a total length of around a kilometre and a half, he said. "The destruction of the network of attack tunnels is an essential part of our policy of systematically harming Hamas' strategic capabilities". Our message to the Gazan leadership and residents of the strip is clear: "invest in the sanctity of life and not in death tunnels".
Israel says it has been developing a new method to identify and destroy such tunnels, though it does not comment on details.
Last week, the IDF struck what many assumed to be a tunnel in the Gaza Strip, following a series of mortar attacks.
The latest tunnel was the third destroyed since late October by Israel, but it comes at a particularly sensitive time.
Cross-border violence between Israel and Gaza has increased since US President Donald Trump's December 6 decision to recognise Jerusalem as the capital of Israel, a move that has angered Palestinians who see the city as the capital of their future state.
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".
The Israeli military said it has destroyed three such tunnels in the past two months, but that it was not seeking escalation.