In 2007 Duncan received a total pay packet of £1.2m and Lygo £888,000.
They have both relinquished their executive bonuses for 2008, which could amount to as much as 30% of their salaries.
Duncan is still in line for a six-figure loyalty bonus, agreed when he joined in 2004.
The news follows reports at the weekend that 91 staff at Channel 4 earn more than £100,000.
Karren Brady, chair of the board's remuneration committee, said: "All our salaries are benchmarked against competitors to make sure we're offering appropriate rates of pay to attract the best staff.
"The board recognises that we are operating in a tough economic climate, and as a result we announced ... that all staff would have their pay frozen for 2009 and the chief executive and director of TV have waived their entitlements under the executive bonus scheme."
Channel 4 has warned that it faces a £150m shortfall in its finances by the time of the digital switchover in 2012.
Lord Carter's interim, released last week, suggests putting a "re-cast" Channel 4 together with BBC Worldwide, the BBC's commercial arm, to plug the expected shortfall as well as keeping other options such as a merger with Five on the table.
At the weekend Five's chief executive Dawn Airey waded into the debate, saying that a merger with BBC Worldwide would not solve C4's problems in the long term.
In an interview with The Sunday Times, Airey said and its German owner 's offer of a tie-up with is a "credible solution".
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