With the economy just now beginning to create jobs in large numbers, the president said a shutdown would damage the recovery.
"For us to go backwards because Washington couldn't get its act together is just unacceptable," he said.
But agreement remained elusive.
Republicans passed legislation through the House at midday to fund the Pentagon for six months, cut $12 billion in domestic spending and keep the federal bureaucracy humming for an additional week.
"There is absolutely no policy reason for the Senate to not follow the House in taking these responsible steps to support our troops and to keep our government open," Boehner said.
Obama flashed a veto threat even before the bill passed on a 247-181, mostly party-line vote. The administration issued a statement calling it "a distraction from the real work" of agreeing on legislation to cover the six months left in the current fiscal year, and there was no indication Reid would allow a vote on it.
As they left the White House after the evening meeting, Reid and Boehner issued a brief written statement that said they had narrowed their disagreements and said they would "continue to work through the night to attempt to resolve" the remaining ones.
Republicans want deeper spending cuts than the Democrats favor and also are pressing for provisions to cut off federal funds to Planned Parenthood and stop the Environmental Protection Agency from issuing numerous anti-pollution regulations.
"They're difficult issues. They're important to both sides and so I'm not yet prepared to express wild optimism," the president said.
For all the brinksmanship — and the promise of more in the Senate on Friday — there was agreement that a shutdown posed risks to an economy still recovering from the worst recession in decades.