Gen. Mark A. Welsh III issued the apology in Japan during his first visit to Asia since assuming the top Air Force job a year ago, Stars and Stripes reported.
"I'm sorry that we as a nation didn't figure out a way to do this better," Welsh told airmen and civilian employees in an all-call at Yokota Air Base.
In an interview before his address, Welsh called sequestration a "brutal mechanism" because it requires across-the-board cuts.
He said it is causing a big headache for Air Force planners and is preventing the Air Force from working with a "predictable top-line number" for the 2014 budget.
Welsh said the topic he spends more time on than anything else is sexual assault in the military.
He said he adamantly opposes an idea proposed by some in Congress of removing authority over prosecution of sex crimes from the chain of command.
""You can't fix it from outside the chain of command," he said.