New York-based JetBlue Airways has defended the cancellation of thousands of flights in severe winter weather in recent days, even as the carrier was criticised for linking the disruptions to new pilot rest rules implemented last weekend.

With sizeable operations in New York John F. Kennedy and Boston, the carrier has emerged as one of the hardest hit carriers as a winter storm wreaked havoc on airline operations in the midwestern and northeastern USA.

JetBlue estimates that it had cancelled about 1,800 flights since 2 January. The carrier suspended operations at Boston and New York JFK, LaGuardia and Newark yesterday, but resumed flights earlier today. JetBlue's chief operating officer Rob Maruster says the airline expects to operate most of its schedule normally tomorrow.

"We absolutely think we did the right thing," Maruster says in a conference call with reporters today.

Maruster adds that closures of New York JFK and new pilot rest rules that went into effect on 4 January had complicated the airline's recovery. Prior to Maruster's comments, JetBlue's blog had cited the new US Federal Aviation Administration (FAA) rules as a factor behind the flight cancellations.

"Even as airports began to reopen though, newly launched FAA regulations on pilot duty times caused delayed flights to quickly turn into cancelled ones," said a JetBlue blog post yesterday.

The blog post attracted a round of criticism on social media, particularly from labour unions. Edward Wytkind, president of Transportation Trades Department, AFL-CIO, tweeted: "Disappointing that JetBlue blogs about delays and blames them on new FAA pilot fatigue rules; I bet their customers want rested pilots."

JetBlue has since sought to clarify its remarks, with Maruster telling reporters today that the new rules were "not a driver in any of our decisions". "It's more of a complicating factor," he says, adding that the airline believes the new rules were "absolutely necessary".

The rules, which were finalised by the FAA in late 2011, limits a pilot's flight time to 8h or 9h depending on when the pilot's flight duty period started. They also require a minimum 10h rest period before a flight, up 2h from previously.

JetBlue had unsuccessfully petitioned the US Department of Transportation in August 2013 seeking flexibility on when to implement the rule. The airline said then that the rule would be implemented during its "most peak travel period of the calendar year" and asked for the FAA to allow it to implement the new rules between 7 January and 31 January.

Maruster reiterates today that the petition had nothing to do with JetBlue's readiness to operate under the new rule. Even as the carrier grappled with flight cancellations in recent days, it contacted the FAA over the 4 January weekend regarding the rules, says Maruster. "We did reach out to the FAA for guidance and consultation to help us recover," he adds. However, the airline and the agency were not able to have a discussion.

JetBlue was not the only US carrier that had to implement the new pilot rest rules. Asked why the airline had cited the new rules as a factor when other carriers have not publicly, a JetBlue spokesperson tells reporters: "We have been the most forthright and transparent."

Maruster says it is too early to assess the financial impact of the flight cancellations. In the fourth quarter of 2012, the carrier sustained a $45 million hit to revenue as a result of Hurricane Sandy.

Source: Cirium Dashboard