Lygo was paid a salary of £773,000, plus £12,000 in benefits and a bonus of £350,000 in the 2008/2009 financial year, according to figures obtained by ITV1's 'Tonight' programme.
Channel 4's chairman Luke Johnson told 'Tonight' that Lygo had volunteered to take a pay cut.
Johnson said: "Last year's total income for [Lygo] included a long-term incentive plan, which was a bonus spread over several years all payable in one year."
The Royal Mail's chief executive Adam Crozier was second on the list, earning £995,000.
Crozier was paid a salary of £633,000, a bonus of £139,000, £17,000 in benefits and a £206,000 cash supplement in place of a pension payment.
The third highest paid public sector worker was Iain Coucher, Network Rail's chief executive, earning £830,000.
The 'Tonight' programme, this week titled 'I'm Paid More than the PM', is on ITV1 at 8pm tonight.