The chief executive of British Airways’ owner has expressed sympathy for striking pilots, and urged – with thinly veiled criticism – the airline’s boss to “get involved” to negotiate a deal.

Willie Walsh, the chief executive of IAG, raised hopes for a resolution to a pay dispute that saw the first pilot strikes in British Airways history, admitting it was “frustrating for me at times” to be on the sidelines of the dispute. He said it was a matter for BA’s management, but added that there was a “deal to be done” and he was “sure pilots’ issues could be resolved”.

Speaking in Toronto, Walsh suggested he would have handled pilots “concerns and frustrations” differently from the BA chief executive, Alex Cruz, adding: “I probably understand their issues better because I used to be a pilot.

“If I were there I would probably want to address those.”

Asked whether Cruz had his backing, Walsh said: “Alex is the CEO. He’s the boss, he has responsibility.”

Invited to express confidence, Walsh said: “I don’t use football analogies.”

BA pilots went on strike for two days last month, causing virtually all of the airline’s scheduled flights to be cancelled on 9 and 10 September. A third day of action was called off but only after BA had cancelled further flights.

IAG issued a profit warning last month, saying the cumulative impact of the industrial action had led to 2,325 flight cancellations over the whole period, and to other losses due to rebookings, with an estimated net financial impact of €137m (£121m).

Speaking on Thursday to mark the launch of the new Airbus A350-1000, which has just entered service on the transatlantic route, Walsh said: “People say when you get to an industrial dispute, there are failings on both sides.

“It’s always easy to say that’s not what I would have done … but they [BA management] made a genuine effort.”

Walsh said there was a fine balance between needing to protect the brand and the financial resilience of the airline.

He said he gave Cruz credit for reaching agreement with other unions in the pay negotiations, adding: “But I would like to see this issue with the pilots resolved, I don’t think it’s in anyone’s interests for it to continue. I’d encourage the BA management team to get involved.”

The pilots union Balpa said it was still hoping to meet BA management for talks at the Advisory, Conciliation and Arbitration Service, but that it reserved the right to set more strike dates. The union has a mandate for further action until January.

Balpa has sought a profit-sharing scheme rather than the 11.5% pay increase over three years in a deal offered by BA. Pilots argue that they should be compensated for cuts to pay and pensions accepted when BA was struggling. Walsh said: “I can understand the argument; I don’t think it’s necessarily accurate.” He said that unions had agreed to pay cuts rather than redundancies.

Walsh added that he did not believe the third runway at Heathrow, where IAG operates more than half of all flights, would now be built. “They now have two major issues that I struggle now to see how they can overcome, the cost of expansion and the environmental impact,” he said.