"I should have told the president about my cancer diagnosis," he told a press conference. "I have apologized directly to President Biden."
Austin effectively vanished from the public eye in late December and early January after suffering complications from treatment for minor prostate surgery on December 22.
Even the White House was not informed about Austin's hospitalization until January 4, while Congress was not told until the following day, and Biden did not learn of the cancer diagnosis until January 9.
Austin said that he did not direct his "staff to conceal my hospitalization from anyone" and he said he had not considered resigning. However, he admitted: "We did not get this right."
He revealed that he is still recovering and has limited use of one leg, using a golf cart to get around the Pentagon building.
Austin's health problems and the unusual secrecy over his treatment comes as US forces are fighting off daily Huthi missile attacks on Red Sea shipping lanes and preparing a military response to the killing of three US soldiers based in Jordan in a drone attack.
The top government military official is also a key figure in attempts by the administration to maintain support for Ukraine's fight against Russian invasion, with Republican members of Congress refusing to pass a new aid package.
The 70-year-old career soldier initially underwent minor surgery to treat prostate cancer on December 22, returning home the following day, but was readmitted due to complications including nausea and severe pain on January 1. He returned to work on January 29.
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