A long article that appeared on New York Times (6/1/2012) does mention that the program was started by President Bush.
According to the article, the Nobel Peace Prize winner president's decision to use the computer virus on Iranian nuclear facilities was made in his first months in office. I remember one of the very first things he did after his inauguration was to bomb Pakistan.
From New York Times (6/1/2012):
Obama Order Sped Up Wave of Cyberattacks Against Iran
By DAVID E. SANGER
WASHINGTON — From his first months in office, President Obama secretly ordered increasingly sophisticated attacks on the computer systems that run Iran’s main nuclear enrichment facilities, significantly expanding America’s first sustained use of cyberweapons, according to participants in the program.
Mr. Obama decided to accelerate the attacks — begun in the Bush administration and code-named Olympic Games — even after an element of the program accidentally became public in the summer of 2010 because of a programming error that allowed it to escape Iran’s Natanz plant and sent it around the world on the Internet. Computer security experts who began studying the worm, which had been developed by the United States and Israel, gave it a name: Stuxnet.
At a tense meeting in the White House Situation Room within days of the worm’s “escape,” Mr. Obama, Vice President Joseph R. Biden Jr. and the director of the Central Intelligence Agency at the time, Leon E. Panetta, considered whether America’s most ambitious attempt to slow the progress of Iran’s nuclear efforts had been fatally compromised.
“Should we shut this thing down?” Mr. Obama asked, according to members of the president’s national security team who were in the room.
Told it was unclear how much the Iranians knew about the code, and offered evidence that it was still causing havoc, Mr. Obama decided that the cyberattacks should proceed. In the following weeks, the Natanz plant was hit by a newer version of the computer worm, and then another after that. The last of that series of attacks, a few weeks after Stuxnet was detected around the world, temporarily took out nearly 1,000 of the 5,000 centrifuges Iran had spinning at the time to purify uranium.
(Full article at the link)
That's an act of war by the way, without declaration. But that's nothing new in the US. Zero Hedge has a post dissecting the NY Times article, here.