President Barack Obama issued a video message late Monday saying the federal government must shut down because members of Congress failed to pass a budget.
"Unfortunately, Congress has not fulfilled its responsibility," he said.
FERC, which governs everything from electricity sales to oil pipeline rates, said its offices would stay open during the shutdown.
"Take notice that, effective as of October 1, 2013 and until such time as the commission issues a notice or otherwise takes action to the contrary, the commission will continue normal business operations and maintain normal business hours," FERC Secretary Kimberly Bose said in a statement Monday.
U.S. Interior Secretary Sally Jewell warned last week that a government shutdown would force her department to operate at the bare minimum.
"When are appropriations are cut, we must scale our resources to the minimum possible level, and that is what we are doing," she said.
The Interior Department manages federal parks as well as oil and natural gas management.
A breakdown from online newspaper Politico said agencies ranging from the U.S. Energy Department to the Environmental Protection agency are affected by the budget stalemate.
The Nuclear Regulatory Agency said it was "prepared for all contingencies." The Department of Energy said it expected its employees to show up for work Tuesday as scheduled for "the immediate future."