He accused the Republican Congress of resorting to "gimmicks and gamesmanship'' instead of meeting the Oct. 1 deadline for passage of the appropriations bills that finance the government.
The resolution extends funding until Oct. 21.
Mr. Clinton also denounced a House GOP plan to delay payments under a program for lower-income working Americans, the earned-income tax credit, in order to save $8.7 billion in fiscal 2000, pushing the cost of the credit into the following budget year.
"I will not sign a bill that turns its back on these hard-working families,'' he said.
With fiscal 2000 tolling at midnight, Senate and House committees tackled different versions of a massive social spending bill, despite veto threats from the White House.
At the start of business on the last day of the old budget year, Congress had completed only five of the 13 annual appropriations bills for the 2000 fiscal year, including one for the District of Columbia that Mr. Clinton already has vetoed.
Just two of the bills have been signed into law, financing the Treasury Department and military construction projects.
For now, neither side was backing down.
The White House wanted higher spending for the environment, housing and other programs, while Republicans were cutting some of Mr. Clinton's initiatives and shifting dollars into their own priorities, such as programs that give states more leeway in apportioning the money.
"We are prepared to veto bills that have the wrong priorities,'' White House chief of staff John Podesta warned during a Wednesday visit to the Capitol.
The labor, health and education spending bill is the biggest of all, totaling about $320 billion.
The House version pared Mr. Clinton's proposals for hiring teachers, expanding Head Start and some health programs for the poor. And though the Senate bill eased many of the House reductions, the White House was threatening to veto either one - chiefly because they provided less than he wants for hiring thousands of new teachers next year.
Republicans charged that the drive for new teachers was a political ploy aimed at playing to teachers' unions and others.
"This has been polled," said Sen. Judd Gregg, R-N.H. "That's why this has been put forward."
On Wednesday, the Senate voted by a near party-line 53-45 for a GOP plan providing $1.2 billion that states could use for hiring teachers, buying school equipment or other educational purposes - contingent on passage of a separate bill creating the new programs. Mr. Clinton proposed $1.4 billion, including money to continue paying the first 29,000 teachers hired last year and to hire 8,000 more, but it was rejected ba party-line 54-44.
Behind the scenes, Republican leaders seemed to be on the verge of resolving two internal GOP disputes that have stalled two major bills.
A long standoff seemed to be over on the Air Force's proposed purchase of its first six F-22 stealth fighters. In a victory for House foes of the war plane, leaders of the two chambers were ready to provide $1 billion to purchase up to six test models, but delay production of the final version for at least a year, said officials speaking on condition of anonymity.
And despite lingering opposition, leaders were also near agreement on a $70 billion agriculture bill that would include close to $9 billion in emergency aid for farmers hurt by low crop prices. It would omit controversial provisions that would have opened food and medicine sales to Cuba and blocked a new federal milk-pricing system.