But embattled US Health and Human Services Secretary Kathleen Sebelius said the numbers indicate continued strong interest among the public with obtaining affordable health coverage.
"The promise of quality, affordable coverage is increasingly becoming reality for this first wave of applicants to the health insurance marketplaces," Sebelius said.
"In every part of our country, Americans are very interested in affordable health care coverage. Even with issues, the marketplace is working and people are enrolling."
Sebelius said, "We expect enrollment will grow substantially throughout the next five months."
Sebelius and other officials said that the ongoing, round-the-clock effort to fix HealthCare.gov has made the experience of using it much smoother for most people, while acknowledging that much work remains to be done to hit a Nov. 30 goal of having the site run smoothly for the "vast majority of visitors."
"The marketplace is working, people are enrolling," said Sebelius, who encouraged people to return to HealthCare,gov and shop for coverage. She also urged people who won't qualify for subsidies because their incomes are too high to shop for plans directly from insurance companies, since only people who will receive those tax credits have to go through HealthCare.gov's data hub at some point.
(Read more: Kentucky sees young women with pricey tastes shopping for Obamacare)
Brushing aside concerns that enrollment was too low, Sebelius cited the experience of Massachusetts, which began its own experiment of mandating health coverage for all state residents in 2006, and built a health exchange to sell insurance to help people meet that mandate.
In its first month of operation, Massachusetts had just .3 percent of what ended up as its total enrollment.
Wednesday's data released showed a wide range of results in individual states.
Among the states whose enrollment is being handled by HealthCare.gov, Florida was the leader, with 3,571 people who had selected an insurance plan by Nov. 2. Another large state, Texas, had 2,991 people select a plan, while Pennsylvania had 2,207 people select a plan.
The worst performer, by far, was Alaska, which had just 53 people select a plan. Wyoming followed, with only 85 people. .
Among states who are operating their own health exchanges, California was the leader, with 35,364 people who had selected a plan by Nov 2. Later Wednesday, California update its current enrollment to more than 59,000,
The Golden State was followed by New York with 16,404 enrollments by Nov. 2, according to federal officials. A distant third place among states operating their own exchanges was Washington, which had 7,091 people.
Under the Affordable Care Act, nearly all Americans must obtain some form of health coverage — either through their employer, private individual insurance, Medicare, Medicaid or military-related insurance — by March 31 or face a tax penalty.
The government-run health-exchanges including HealthCare.gov and the state marketplaces are selling insurance offered by a variety of insurers at competing prices to help people meet that mandate if they lack coverage, or are looking for a different plan than the one they have now.
Experts estimate that about half of the people who will ultimately buy coverage through one of those exchanges will qualify for government subsidies to offset the cost of their plans.
—By CNBC's Dan Mangan. Follow him on Twitter