The effects of Tuesday's strike by Swiss pilots, which led to 128 cancelled European flights, have run over into Wednesday with 14 further flights being dropped.
Swiss International Air Lines said it intends to claim damages from the Swiss Pilots Association (SPA) for the work stoppage which analysts say damaged the airline's image.
"The strike has led to some reorganisation that was not foreseeable yesterday," airline spokesman, Jean-Claude Donzel, said about Wednesday's additional cancellations.
"In a few cases the crew wasn't in the right place or was missing." Donzel said he expected the situation to "normalise" over the course of the day.
The SPA, one of two pilots' unions at Swiss, voted to go on strike after the airline failed to meet its demands for improved salaries and benefits.
The 78 pilots who took part in the action want their pay package to match those of pilots flying long-haul routes.
SPA maintains that its members are being discriminated against in terms of pay and conditions. Most recently, disagreements have arisen over a new labour contract between the airline and pilots.
The union members are former Crossair pilots. Swiss was founded in 2002 following the merger of the regional carrier Crossair and the remains of Swissair, which collapsed a year earlier.
The strike involved short-haul Avro airliners and the majority of cancellations were at Zurich airport. About 9,000 passengers were affected.
Thomas Isler, SPA president, said they had decided on Tuesday evening to end the strike, although an ultimatum by the airline to end the action by 6pm was ignored. Isler said the Swiss management had not presented any concrete suggestions.
"The only thing we received today was threats," he said, adding that one was for a claim for damages.
Sepp Moser, an aviation expert told swissinfo that Tuesday's strike would not greatly harm Swiss financially but it would cause much greater damage to the company's image.
"However, if this dispute is not resolved soon it may have bigger implications in the future," he added. Lufthansa have not yet taken over Swiss – they only have a 49 per cent stake at the moment. They do have the option of completing the takeover in the future, but they have set in place a number of conditions before they are willing to do this.
Moser said one of those conditions is that the ongoing pilots dispute gets resolved and he warned that if that did not happen then there was a danger that Lufthansa would rethink its plans.
"The Swiss management have not done enough to find a solution," he said. "In fact, they even disrupted plans to set up an arbitration committee at the end of last year. They have been shooting themselves in the foot over this issue."
However, Jérome Schupp, an aviation analyst from Bank Syz in Geneva, didn't think Swiss would be damaged too much by this strike. "Air France is hit by a strike every year and they are still in a very healthy position," he said.
"But unions and workers act differently in France and it is normal to see strike action. In Switzerland, unions and management spend much more time negotiating and only very rarely will you see industrial action.
"From this perspective it must be of some concern to the Swiss management that the unions have run out of patience."
Former national carrier Swissair collapsed in 2001.
With government backing, Swiss was launched on March 31, 2002.
In March 2005 the airline announced its takeover by Lufthansa for €279 million (SFr430 million).
After receiving antitrust clearance in July of the same year, the German airline increased its stake to 49 per cent, which it is expected to increase to 100% by the end of 2006.
More than 140 flights were cancelled on European routes.
Swiss set up a telephone hotline on +41 44 564 17 47 to offer alternative travel arrangements.