Duncan was challenged over the salaries by the House of Commons select committee for culture, media and sport.
is currently seeking financial assistance to make up a £150m budget shortfall it claims it will face by 2012.
The salaries were defended by Duncan who replied: "We need good people to do the job. We have had a very strong creative and commercial period."
"Having said that, reflecting the difficult impact of the recession on Channel 4 certainly all of our better paid people didn't take a bonus last year and we have implemented a pay freeze."
Around 80 employees at Channel 4 earn over £100,000 a year while Duncan is on a current basic salary of £670,000 and is also entitled to a £225,000 loyalty bonus.
The Commons exchange comes as Channel 4 looks to tie up with , with Duncan stating an agreement could take shape within the coming weeks.
However, efforts to produce a memorandum of understanding between the two have stalled on the BBC's demand Channel 4 should waive any further claim to license fee cash.
Channel 4 chairman Luke Johnson told the committee that he would not agree to any deal that left the broadcaster without license fee funding.
Duncan and Johnson also criticised the BBC for using its financial weight to outbid Channel 4 for US dramas.
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