A UN team of international bomb disposal experts has been working to neutralise unexploded munitions in the strip since major fighting ceased last month.
Peter Lerner, an Israeli defence ministry official, told Reuters that Israel had been notified that a number of bombs had disappeared.
"We were told of the disappearance of the bombs, our understanding is that Hamas took them," he said.
Israeli air raid
Meanwhile on Wednesday, the Israeli military dropped more munitions in the Gaza Strip, hitting two targets in an air raid but causing no casualties according to Palestinian residents and Hamas security officials.
An Israeli army spokesman confirmed that aircraft had hit targets in Gaza but gave no further details.
Residents said one strike targeted tunnels which run under the Egyptian border in the town of Rafah and another hit an already bombed-out security compound in the town of Khan Younis.
The strikes came after the firing of a mortar round into Israel on Tuesday evening.