Brigades, the militant group said Thursday.
The three members of the Brigades' 15-member military council were killed in a bombing in Rafah in southern Gaza, according to Hamas.
The announcement of their deaths come the day after Hamas said an Israeli strike had killed the wife and 7-month-old son of Mohammed Deif, the head of the military wing. The strike failed to kill Deif, Hamas said.
Role in capture of Israeli soldier
The militant group, which controls Gaza, said the leaders killed overnight were Mohammed Abu Shamala, Raed al-Attar and Mohammed Barhoum.
Hamas vowed revenge for their deaths.
"The assassination of the Qassam leaders is a great Israeli crime that will not succeed in breaking the will of our people or even weaken the resistance, and Israel will pay the price," spokesman Abu Zuhri said.
Al-Attar, the commander of the Qassam Brigades in Rafah, is believed to be the most senior of the three.
The Israeli military said it had confirmed that it had killed al-Attar and Abu Shamala, describing them as "high-ranking Hamas commanders responsible for major terror attacks against Israelis."
Al-Attar played a "major role" in the capture of the Israeli soldier Gilad Shalit in 2006, the Israel Defense Forces said on its Twitter account. Shalit was held captive until a deal was struck for his release in 2011 in exchange for more than 1,000 Palestinian prisoners.
"This morning's strike sends a clear message to those responsible for planning attacks," IDF spokesman Lt. Col. Peter Lerner said in a statement. "We will strike those that have terrorized our communities, towns and cities, we will pursue the perpetrators of abduction of our soldiers and teenagers, and we will succeed in restoring security to the State of Israel."