There are about 40,000 medications used in hospital settings on a regular basis, and fewer than 200 of those have been in short supply, said Sebelius.
While the number is relatively small, some types of drugs are first-line treatments that are essential to saving lives, she said.
According to Bonnie Frawley, a pharmacist at Brigham and Women's Hospital in Boston, doctors at the hospital were nearly one week away from canceling heart surgeries this summer because of a drug shortage.
The hospital had a shortage of a hard-hitting antibiotic called Gentamicin, which is the primary therapy used to for bacterial infections resistant to most other types of antibiotics, Frawley said.
"We were forced to use other antibiotics that were second-line therapy," Frawley said at the press conference. "This is a concern because health care providers may not have experience using alternatives."
Since these medications are mainly housed in hospitals, most patients won't know they can't have them until they really need them.
Maggie Heim, 58, of Hermosa Beach, Calif., was diagnosed with recurrent ovarian cancer in July 2011, and told by her doctors at Cedars Sinai Medical Center that she would have to wait to receive chemotherapy since the hospital had a shortage chemotherapy agent doxorubicin.
"I thought it was going to be available in two weeks, so I thought I'll just miss the first round of therapy," said Heim, who said she never knew about a shortage problem before her experience.
But more than three months later, the hospital has still not received enough doxorubicin.
"It was very disturbing to me to do research and see how many women with cancer are affected," said Heim, who is a member of the patient online community Inspire. "I was angry, but I was also disappointed that we as a country could not get our acts together."
Heim was offered an alternative drug that worked for her cancer, but she said many other women she has connected with after her experience need the drug to save their lives.
"How can our country do so much and so little?" she said.
ABC News' Mary Bruce contributed to this report