Tim Byrne, Airtours' finance director and managing director-designate, said: "At the end of the day, this was not the right decision." He stressed that the appeal would centre on the ability of European companies to compete globally.
Airtours will argue against the precedent set by the Commission's 22 September ruling, which blocked the takeover on the grounds that it could create a potential oligopoly in the UK travel market. Mr Byrne said: "This has implications for all European businesses, and for how they can compete against their US rivals... What we want to find out is: 'What are the rules?'"
One corporate lawyer said the case had created "a huge amount of uncertainty about the merger control process". He said it remained unclear whether the Commission now intended to block all proposed takeovers that would cut four major competitors to three.
Mr Byrne said Airtours had received encouragement from a number of groups outside the holiday sector, and warned that if the First Choice decision was upheld, it could derail the merger plans of companies such as Carlton Communications and United News & Media.
Airtours' senior managers debated at length whether to proceed with the appeal, which could take two to three years and will cost the company about pounds 1m a year. Mr Byrne said: "We were concerned that we made the right business decision, and that it wasn't emotional."
Separately, Airtours refused to confirm or deny rumours that it is in talks to acquire Holidaybreak, a holding company that provides camping and mobile home services.
Airtours shares closed down 11.75p at 403p.