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A backpack found floating in the waters around a Sydney Harbour navy base caused a bomb scare and evacuation today.

After a three hour investigation, police allowed evacuated navy officers to return to the HMAS Kuttabul base on Garden Island.

Hundreds of uniformed military personnel were evacuated from the site – soon after the suspicious package was discovered.

The red and black backpack was taken ashore about 8.30am and the bomb squad, Kings Cross police and rescue coordinators were called to lead an investigation.

“There was a backpack floating in the water,” Detective Inspector Simon Jones of Kings Cross Police said.