"The American people understand that we have got a big hole we have got to dig ourselves out of but they don't like the idea that people are digging a bigger hole," Obama said after meeting Geithner at the White House.
"There will be time for them to make profits, and there will be time for them to get bonuses. Now is not that time"
Obama's comments came in swift response to a report from the New York state comptroller that employees of the city's financial world had made huge gains last year.
The president said Geithner had already been forced to step in to stop one company from taking delivery of a new corporate jet even after receiving billions of dollars in government bailout money.
"There will be time for them to make profits, and there will be time for them to get bonuses," Obama said. "Now is not that time."
Obama's outrage on Thursday overshadowed his announcement of forthcoming plans to get more credit flowing to consumers.
He said his plan to reignite growth would include the massive stimulus package moving through congress as well as steps to unfreeze credit markets and overhaul financial regulations.
The US senate is preparing to debate the roughly $900bn stimulus plan, after the House of Representatives passed a version of it on Wednesday.
The Obama administration is considering a range of ideas including the possibility of a government-run "bad bank" to buy up the toxic assets.
Obama, who blames lax regulation on Wall Street for the economic crisis, said a comprehensive plan to revamp the financial rules would be rolled out in the coming weeks.
He said this is "so that the American people will have a clear sense of a comprehensive strategy designed to put people back to work, reopen businesses, get credit flowing again".