The army issued orders to Israelis living on the Gaza periphery to be ready to enter the shelters in case rockets start falling from Gaza.
A video released by the Israeli military shows two men in a watchtower, said to be in northern Gaza, and puffs of smoke as one appears to open fire.
Hamas's military wing, the Izz al-Din Qassam Brigades, confirmed two of its members were killed, but said the border post was hit during an "exhibition" by a naval commando unit that was being watched by several Hamas leaders.
"The resistance can not allow the occupation to impose a policy of bombing sites and targeting fighters without paying the price", it said in a statement.
In turn, earlier, the UN General Assembly adopted a resolution condemning Israel for actions in Gaza.
At least 158 Palestinians have been killed in four months of weekly border protests and one Israeli soldier was shot dead by a Gaza sniper. Sources said that Hamas is unwilling to enter into any negotiations or provide any information about the Israeli soldiers detained, agreeing only to a prisoner exchange in return for the freeing of prisoners rearrested after the Gilad Shalit deal in 2011. It deemed Israel's shelling of them a "criminal act".
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