Thompson was appearing on a special guest edition of BBC Radio 4's Today programme edited by author PD James.
During the interview, the writer questioned whether the BBC's top 37 managers should all be allowed to earn more than the prime minister.
The director general's salary for 2008/9 was £834,000, over four times higher than Gordon Brown's pay packet of £197,689. Last month, the BBC also published expense data for all its top managers, including Thompson's claim of £647.50 for a two-night stay at the famed Bellagio hotel in Las Vegas.
In response, Thompson stressed that despite the high levels of pay, the BBC was still losing its key talent to the commercial market where they could earn more money.
Lady James, a former BBC governor, also expressed her belief that the BBC had lost its way. She said that while some BBC programming was of a high quality, other material was more tenuous in its value as public service broadcasting.
The novelist asked Thompson how he could justify the "extraordinarily large" salaries paid to top BBC management, when there was significant concern about it among some licence fee payers.
Thompson responded by saying that the BBC faces strong competition from commercial operators to secure the top talent who can deliver the best programmes and services.
He said that controller of BBC One Jay Hunt, who oversees a programming budget of around £1bn, took a pay cut when she joined the corporation. Most other managers, he added, also receive less than their equivalent commercial market rates.
In October, the BBC Trust backed Thompson's plans to cull over 100 senior BBC managers and also trim top executive pay by 25% over the next three and a half years.