The journalist, one of the most familiar faces on the BBC's news programmes, said the issue of high pay had given the corporation's opponents "sticks and stones to chuck at us".
Director-general Tony Hall introduced a cap on pay-offs of £150,000 when he took over following the furore over the £470,000 paid to his predecessor George Entwistle.
Mr Entwistle was paid a year's salary when he left the BBC's top job, even though he had only been in place for 54 days before resigning over his handling of the Jimmy Savile scandal.
Other senior figures who walked away with huge sums include former chief operating officer Caroline Thomson, who got £680,000, and deputy director general Mark Byford, who left with a total payout of £949,000.
Bowen said: "The over-remuneration of people was a huge mistake and it's caused massive damage to the BBC. It's caused it internally, because the vast majority of people who work at the BBC do not get brilliantly paid.
"But the massive salaries given to top management angered people on the shop floor."