The Israeli military said the target was a camp used by militants associated with the Fatah group of Palestinian leader Mahmoud Abbas.
An Israeli army spokesman said earlier in the day soldiers had fired on a car occupied by Palestinian militants who had fired rocket near the border with Israel.
The latest attacks come a day after six Palestinians, including a child, were killed near Rafah in the Gaza Strip.
Palestinian Prime Minister Ismail Haniyah has accused the United States and the European Union of blackmail after both announced they were suspending millions of dollars in aid to the Palestinian Authority because of Hamas's refusal to recognise Israel's right to exist.