Israeli military spokesman Lt. Col. Jonathan Conricus told CNN the strike was carried out Saturday with "necessary coordination" with Egypt.
Sources told the Palestinian News Network no one was injured in the strike.
"This is a blatant violation of Israeli sovereignty, endangering the citizens of Israel and sabotaging the humanitarian efforts that Israel is making for the citizens of Gaza," an IDF statement read.
"The terrorist organization Hamas is responsible for everything happening in and out of the Gaza Strip," the IDF said.
Cornricus said that if the tunnel was only to smuggle harmless goods, there was no need for it to go under Kerem Shalom.
This is the third tunnel into Gaza Israel has destroyed in two months.
The IDF will continue its efforts above and below ground to thwart any attempts to harm Israeli civilians pic.twitter.com/YGtJk37MH2— IDF (@IDFSpokesperson) January 14, 2018