Heapy said travel firms and their customers shouldn't be left to "pick up the pieces" when aspects of what he described as "critical national infrastructure" fail, and has called for "proper answers".
Chief Executive Heapy revealed more than 7,000 Jet2 customers were affected at the peak of the disruption last week when Nats suffered a technical issue on Tuesday (8 September).
The government last week gave Nats Chief Executive Martin Rolfe a week to explain the meltdown; more than 2,000 flights were cancelled during the resultant disruption.
After what it described as a "round the clock" operation to get passengers on their way, Jet2 on Tuesday (15 September) said it was seeking "urgent, clear action" to improve Nats so holidaymakers "can look forward to their trips without the fear of critical infrastructure failures causing unnecessary stress, delays and uncertainty".
Jet2 put on more than a dozen additional flights using "all available spare aircraft capacity" and drafted in extra teams to fly customers home from Greece, Turkey, Spain and Malta. It also arranged overnight hotel accommodation, where possible, to support stranded passengers.
Despite the disruption being caused by a national infrastructure failure, the burden falls on airlines operationally and financially to sort out. Jet2 has promised those passengers whose travel plans were affected full refunds.
“This latest failure caused significant disruption to thousands of our customers through no fault of their own, and once again airlines, colleagues and customers were left to pick up the pieces because critical national infrastructure failed," said Heapy.
"That is completely unacceptable and holidaymakers deserve much better. The government has a direct responsibility given its 49% ownership of Nats, and with customers needing confidence and airlines needing certainty, proper answers are required following this latest failure."
Heapy also paid tribute to Jet2's workforce. "Our teams went above and beyond to look after customers, get people home and recover our operation," he said. "By arranging extra flying and deploying every available resource, we have been able to help thousands of customers return home as quickly as possible.
"I would like to thank our fantastic colleagues... their effort has been exceptional, but the simple fact is that hardworking holidaymakers should never have been put in this position in the first place."