Carne stood to receive a £34,000 performance-related bonus on top of his £675,000 a year salary.
But in light of the huge disruption at King’s Cross and Paddington - which left thousands of passengers scrambling to get home just after Christmas - he has said he will not accept it.
Carne, who came under fire for being on holiday at the time, told Sky News: "I'm accountable for the performance of the railway. In my view, the performance over the Christmas and New Year period was not acceptable."
"And I've decided I should not take the bonus for this year."
He added that there was "never a good time" to do the engineering work and that the King's Cross plan "didn't work out in a satisfactory way".
In a statement, the rail chief admitted “the last few days for many passengers have been miserable”
Carne has commissioned a report into “the sequence of events and associated decision making that led to the problems experienced and to advise of any immediate steps that we need to take”.
The report, by Network Rail’s infrastructure projects director Dr Francis Paonessa, is due next week and Carne has committed to publishing the findings.
"The events over the Christmas period highlighted the unacceptable impact on the travelling public when plans go wrong,” he said.
“I therefore propose that there should also be a broader, industry-wide review, into the timing of our major works programmes and the passenger contingency arrangements for such works.
“Our railway now carries more passengers than ever before in history. Passengers rely on the railway. We have an obligation to manage the essential safety maintenance and renewal activity that is required and we need to do this in a manner that minimises the overall impact on society at large. I will discuss this review with industry parties in the coming days before formalising the terms of reference for this review."