The memo, obtained by The Associated Press, said incomplete testing created uncertainties that posed a potentially high security risk for the website. It called for a six-month "mitigation" program, including ongoing monitoring and testing.
It revealed that the troubled website was granted a temporary security certificate on Sept. 27, just four days before it went live.
Republicans argue the troubled website' glitches are proof the government is incapable of managing the complex health care program.
"You accepted a risk on behalf of every user ... that put their personal financial information at risk," Rep. Mike Rogers told Sebelius, citing the memo. "Amazon would never do this. ... This is completely an unacceptable level of security."
Sebelius countered that the system is secure. Added spokeswoman Joanne Peters: "When consumers fill out their online...applications, they can trust that the information they're providing is protected by stringent security standards and that the technology underlying the application process has been tested and is secure."
Republicans opposed to Obama's health care law are calling for Sebelius to resign.
HealthCare.gov was intended to be the online gateway to coverage for millions of uninsured Americans, as well those who already purchase their policies individually. Many people in the latter group will have to get new insurance next year because their policies do not meet the standards of the new law.
Starting Jan. 1, most Americans will be required to carry health insurance or face fines. At the same time, insurance companies will no longer be able to turn away people in poor health. The law provides subsidized private insurance for middle-class people who don't get health care on the job. Low-income people can access an expanded version of Medicaid in states that agree to expand that safety net program.
Lawmakers wanted to know how many people have enrolled in plans through the health insurance marketplaces. Sebelius stuck with the administration response, promising to release the data in mid-November.
Obama's White House legacy depends heavily on whether his massive overhaul of the U.S. health care system will succeed.
Sebelius testified as another controversy brewed over a wave of cancellation notices hitting small businesses and individuals who buy their own insurance. Republicans say that contradicts one of Obama's earliest promises about the health law: You can keep your plan if you like it.
The cancellations affect some of the 5 percent of Americans who buy health insurance on the private market.
"If you're getting one of these letters, just shop around in the new market place," Obama said. "That's what it's for."
He pointed to benefits already available under the health care law, including ending discrimination against children with pre-existing conditions or people with mental health issues.
He spoke in Massachusetts, where the state's health care coverage provided the model for the federal overhaul. Republican Mitt Romney, who lost to Obama in the 2012 election, was Massachusetts governor and signed the state's health care bill into law.
But in a statement Wednesday, Romney said he believes "a plan crafted to fit the unique circumstances of a single state should not be grafted onto the entire country."
The federal law doesn't create a government-run system like Britain's, but it does mandate that large employers provide insurance and that everyone must be insured or face tax penalties. Those who can't afford insurance can receive subsidies in states that accepted federal money for an expansion of the Medicaid program for low-income Americans.
Several Republican-governed states rejected the federal money and are not expanding Medicaid.
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AP writers Stephen Ohlemacher, Ricardo Alonso-Zaldivar, Laurie Kellman, Jack Gillum and David Espo contributed to this report.
