The Environmental Protection Agency and Department of Housing and Urban Development listed only six percent of their employees as essential, and therefore permitted to work during the impasse. James R. Clapper, director of national intelligence, said about 70 percent of civilian employees in agencies under his control had been sent home.
By contrast, about 86 percent of employees of the Department of Homeland Security remained on the job, and 95 percent at the Veterans Affairs Department.
One furloughed employee, meteorologist Amy Fritz, said, "I want to get back to work." At a news conference arranged by congressional Democrats, the 38-year-old National Weather Service employee said she has more than $100,000 in student loan debt and is looking at ways to cut her budget.
In an interview with CNBC before meeting with lawmakers, Obama said he would not negotiate with Republicans until the government is reopened and Congress votes to raise the debt limit.
"If we get in the habit where a few folks, an extremist wing of one party, whether it's Democrat or Republican, are allowed to extort concessions based on a threat (to) undermine the full faith and credit of the United States, then any president who comes after me, not just me, will find themselves unable to govern effectively," he said.
"The White House said Obama would have to truncate a long-planned trip to Asia, calling off the final two stops in Malaysia and the Philippines.
The shutdown also intruded into the race for governor of Virginia.
Terry McAuliffe, the Democrat, said he supported legislation to guarantee retroactive pay for furloughed federal employees. The Republican contender, Ken Cuccinelli, called on members of Congress to decline their pay as long as the shutdown lasts.
The House sidetracked legislation Tuesday night to reopen some veterans programs, the national parks and a portion of the Washington, D.C., municipal government. All three bills fell short of the two-thirds majority needed when Democrats voted overwhelmingly against this.
Republicans tried again, this time under rules requiring only a simple majority. The parks measure was approved on a vote of 252-173, with 23 Democrats breaking ranks and voting in favor. The vote to reopen NIH was 254-171. The House also voted to allow the Washington, D.C., government to use the taxes it collects to operate programs.
Votes were deferred on more bills, one to assure pay for members of the National Guard and Reserves and another to allow some veterans programs to resume.
The NIH bill was added to the day's agenda after Democrats had said seriously ill patients would be turned away from the facility's hospital of last resort, and no new enrollment permitted in experimental treatments.
Democratic Rep. Louise Slaughter of New York said the Republican response was a ploy. "Every time they see a bad headline they're going to bring a bill to the floor and make it go away," she said.
Some Republicans took obvious pleasure in the rough rollout Tuesday of new health insurance markets created under Obama's health care law. Widespread online glitches prevented many people from signing up for coverage that begins in January.
Rep. Trey Radel of Florida said a 14-year-old could build a better website "in an afternoon in his basement."
At issue is the need to pass a temporary funding bill to keep the government open since the start of the new budget year on Tuesday.
Congress has passed more than 100 temporary funding bills since the last shutdown in 1996, almost all of them without controversy. The streak was broken because conservative Republicans have held up the current measure in the longshot hope of derailing or delaying Obamacare, just as the health insurance markets at the heart of the law opened on Tuesday.
Associated Press writers Andrew Taylor, Donna Cassata, Henry Jackson, Julie Pace, Jessica Gresko, Darlene Superville and Seth Borenstein contributed to this story