Hamas named the men as Mohammed Abu Shammala, Raed al-Attar and Mohammed Barhoum and said they were killed in the bombing of a house in the southern town of Rafah. All three were described as senior Hamas military figures.
The Israeli military and Shin Bet, the internal security service, confirmed two of the men were targeted, in what would constitute the killing of the most senior Hamas leaders since Israel launched its offensive in Gaza on July 8.
Israeli Prime Minister Benjamin Netanyahu praised the "outstanding intelligence" and said in a statement the Hamas leaders "planned deadly attacks against Israeli civilians".
After six weeks of conflict in which more than 2,000 Palestinians have been killed, most of them civilians, Israeli air strikes since a 10-day ceasefire collapsed on Tuesday appear to have been focused more intently on Hamas's armed wing.
Late on Tuesday, the Israeli air force bombed a house in northern Gaza, an attempt, Hamas said, to assassinate Mohammed Deif, its top military commander. His wife and seven-month-old son were killed but he escaped.