Witnesses said Jamal Abu Samhadana, also a member of the Popular Resistance Committees group, was among four people killed in a PRC-run camp near Khan Yunus.
An Israeli military spokeswoman confirmed the strike late on Thursday, but said it was aimed at the camp rather than at any specific resistance fighter.
Hamas appointed Abu Samhadana as supervisor over the interior ministry, which oversees security services, in April.
The strike angered Mahmoud Abbas, the Palestinian president, who has been trying to salvage peacemaking with Israel since Hamas defeated Fatah in the January elections.
The PRC is a coalition of resistance groups that have spearheaded a more than five-year-old Palestinian uprising. Since Israel quit Gaza last year after 38 years of occupation, it has played a leading role in cross-border rocket launches.
The PRC pledged fresh attacks on Israel to avenge Abu Samhadana's death.
A spokesman for the group said: "The Zionist entity and Zionist settlements near Gaza will not feel security and safety any more. Our rockets will rain into the Zionist entity and our heroes will blow themselves up among their dirty bodies."