The US administration also refused to give permission for Israeli fighter jets to fly over Iraq — the quickest route to Iran, it said.
Israel, the region's sole if undeclared nuclear armed state, considers Iran its main strategic threat because of its own atomic programme, which Israel and its main US ally suspect is aimed at developing weapons.
Iran has repeatedly denied the allegations, insisting it wants only to provide electricity for its growing population when its fossil fuels run out.
Military experts believe the GBU-28 "bunker busters" Israel had requested could be effective against Iran's underground uranium enrichment facility at Natanz in central Iran.
The GBU-28 is a 2.2-tonne, laser-guided, conventional munition equipped with a powerful warhead that can burrow through more than six metres (20 feet) of concrete and up to 30.5 metres (100 feet) of hard ground.
Israeli Defence Minister Ehud Barak said after a meeting with US Secretary of State Condoleezza Rice last month that the United States "do not want, for the time being, any (military) action against Iran" but that Israel kept all options open.
While denying the requests for "bunker-buster" bombs and refuelling planes, the US administration has agreed to help reinforce Israel's defences.
An advanced US radar system is to be stationed in Israel which would double the 2,000-kilometre (1,250-mile) detection range of missiles launched from Iran. The system would be connected to an US early warning system, a senior defence official told AFP.
The Israeli defence ministry did not immediately comment on the newspaper report.
