The report, authored by Bowles and his co-chairman former Sen. Alan Simpson, came under fire last week from a broad range of groups, including several tax organizations that faulted the plan for raising taxes across the board even though the brackets were lowered to compensate for the changes.
The mortgage-interest and the employer-provided deductions were targeted by critics for providing tax cuts for the wealthy and tax increases for the middle class.
"Let's bring rates down to 8, 14 and 23, and then, if you want to add back something like the mortgage-interest deduction, then tell us how you're going to pay for it," Bowles said, suggesting that compromise on the report is possible.
From early indications, many changes are likely needed for the report to gain support of 14 of 18 members of the fiscal commission by the Dec. 1 deadline.
Even though that majority support appears dim, Bowles was "hopeful" an agreement could be reached on a plan that could be sent to Congress.
"What we're trying to do is to listen to other people's ideas to see how we can improve this package," he said.
"We've gotten lots of cooperation. We've spent months and months listening to people on both sides of the aisle. And that's the way you build up trust and you find compromise and you find a way to really solve what is a very, very difficult problem."
Still, without enough support, Bowles said the commission has started laying a path to smaller deficits and a balanced budget.
"Then what we've done is lay a predicate for this next Congress to deal with where we have $3 of spending cuts for every dollar of revenue increase," he said.