Gibbs also said Obama backed moves to strip the power to select a senator from Blagojevich and convene a special election for the vacant seat.
"The president-elect believes that the general assembly should consider the issue and put in place a process to select a new senator that will have the trust and confidence of the people of Illinois," Gibbs said.
Blagojevich arrived at his office for work on Wednesday and has so far refused to resign his position.
Al Jazeera's Rob Reynolds says Obama had been under considerable pressure to say more on the scandal after a number of Illinois politicians and Republican politicians condemned the governor's alleged actions.
Obama himself said on Tuesday that he was unaware of any alleged corruption by and had had "no contact" with either the governor or his office.
|Blagojevich also allegedly discussed taking the
senate seat himself [AFP]
"Like the rest of the people of Illinois, I am saddened and sobered by the news that came out of the US attorney's office today," the president-elect said.
The FBI affidavit says Blagojevich allegedly discussed the possibility of receiving a substantial salary working for a non-profit foundation or labour union and a cabinet post or ambassadorship for himself in return for appointing Obama's replacement.
The 51-year-old was also charged with illegally threatening to withhold state assistance to the owners of the Chicago Tribune newspaper and reportedly demanding that members of the newspaper's editorial board who had been critical of him be fired.
Blagojevich also allegedly discussed placing his wife on corporate boards, where he speculated she might get paid as much as $150,000 a year.
"If I don't get what I want and I'm not satisfied with it, then I'll just take the senate seat myself," Blagojevich said, according to court papers.
Patrick J Fitzgerald, a prosecuting attorney, said in a statement that "the breadth of corruption laid out in these charges is staggering."
However Fitzgerald said that Obama was in no way implicated in the case.
"I should make clear the complaint makes no allegations about the president-elect whatsoever," he said.
Among those being considered for the senate post included Danny Davis and Jesse Jackson Jr, both US congressmen, the Associated Press news agency reported.
John Harris, Blagojevich's chief of staff, was also arrested and both men have also been charged with conspiracy to commit mail and wire fraud and solicitation of bribery.