The defections by ConocoPhillips, America's third largest oil company, Caterpillar, which makes heavy equipment, and BP rob the US Climate Action Partnership of three powerful voices for lobbying Congress to pass climate change law.
They also undercut Obama's efforts to cast his climate and energy agenda as a pro-business, job-creation plan.
Only hours earlier, Obama and other cabinet officials had made a high-profile announcement that $8.3bn (£5.3bn) was being awarded in loan guarantees for a company building the first new nuclear reactors in America in nearly 30 years.
But the loan decision in favour of Southern Company, which was framed by the White House as a kick-start for new nuclear plants, was upstaged by the departure of the big three firms from the climate partnership.
The House of Representatives passed a climate change bill last June, but the effort has stalled in the Senate.
'House climate legislation and Senate proposals to date have disadvantaged the transportation sector and its consumers, left domestic refineries unfairly penalised versus international competition, and ignored the critical role that natural gas can play in reducing GHG emissions,' said the ConocoPhillips chairman and chief executive, Jim Mulva, in a statement.
Officials from BP and ConocoPhillips said that the proposals before Congress for curbing greenhouse gas emissions did not do enough to recognise the importance of natural gas, and were too favourable to the coal industry.