Although the scheme would help to cut back Europe's carbon dioxide emissions as a whole, the "burden of reduction" would fall on ground-based industries, while the aviation industry would buy emissions permits under the scheme to continue its expansion, said Andrew Sentance, who is also BA's head of environmental affairs.
Mr Sentance's admission will be seized on by environmental campaigners, who claim that although including aviation in the EU scheme is being trumpeted as a major step forward, it will do nothing to make actual cutbacks in levels of aircraft emissions - the fastest-growing sector of all greenhouse gases.
As a result of this, the environment committee of the European Parliament is proposing that instead of putting aviation into the general ETS as presently constituted, there should be a special scheme just for the aviation industry.
Under such a scheme, airlines would have to compete only with one another for pollution permits, and not with industry in general, and so would be under much fiercer pressure to cut damaging exhaust emissions.
The proposal, strongly opposed by airlines including BA, will be voted on by the parliament in Strasbourg next week. Although it will not automatically become binding EU policy if adopted, it is likely to have a major influence on the final decision of the European Commission on aviation and the ETS, which is expected in the autumn.
Emissions from aviation are an increasingly hot topic in the drive to contain global warming, Accounting for a little less than six per cent of total emissions in the UK, the burgeoning growth of air passenger traffic means they will zoom up to become an increasingly large proportion of the total in the coming decades.
Although new carbon limits are being set for EU member states for the next stage of the existing ETS beginning in 2008, the earliest that aviation could be included is 2012, given the time it would take to pass the necessary laws.
The UK airline industry is divided over whether carbon trading is a good idea. BA and easyJet strongly support emissions trading to head off the draconian alternative of a tax on aviation fuel to curb air travel. The UK airports operator BAA also backs the idea. But Ryanair is opposed and bmi, the second biggest airline at Heathrow, remains to be persuaded either way.
BA thinks any scheme would have to be restricted to point-to-point travel within Europe because of the difficulty of trying to impose carbon limits on overseas airlines, particularly US ones. But easyJet wants it to cover all airlines flying into and out of Europe, on the grounds that air travel within the EU accounts for only 25 per cent of total carbon emissions. Along with BA, it wants a "benchmarking" system so airlines with younger, less polluting aircraft fleets get preferential treatment when permits are allocated.
Although bmi gave cautious support yesterday to carbon trading, Sir Michael Bishop, the chairman, remained "neutral". "I'd like to see more research before we are put on the cross and locked into a scheme which could last 25 or 30 years. Agriculture accounts for a much bigger proportion of UK carbon emissions but you never see farmers being held to account," he said.
Sir Michael also questioned how much political will there would be for including aviation in the ETS. "I'd like to see the politician who bans cheap air travel. There are no votes in that."
In September the Tyndall Centre for Climate Change Research at the University of East Anglia forecast that if the UK was to meet its climate change target of cutting back total CO2 emissions by 60 per cent by 2050, the aviation industry would account for 100 per cent of Britain's allowable emissions by that date, if air travel continued to grow at its current rate. "Everyone else's carbon emissions will have to go to zero to allow for aviation pollution," the centre said.
Air passenger traffic is forecast to more than double in the UK in the next 25 years, from 180 million to 475 million passengers per annum.
Asked yesterday if joining the EU trading scheme would allow aviation emissions to continue growing, Mr Sentance said: "Yes, it would allow them to continue to grow. But it would allow emissions from other sectors to continue to grow as well, if they want to buy the permits. What it would do is ensure that globally, the target of a 60 per cent reduction in emissions could be achieved."
But Mr Sentance disputed the centre's projections, and said by 2050 UK aviation emissions would range from 17 per cent of the total - under a scenario of low traffic growth and high fuel efficiency - to 46 per cent of the total - under a scenario where growth was high and fuel efficiency low.
He also rejected environmentalists' claims that the scheme would fail in its object if it did not force a cutback in the amount of CO2 jet aircraft inject directly into the stratosphere each day.
Green campaigners were wrong to focus on aviation, "just one sector", he said. "They should look at the global picture. The emissions trading scheme is the most effective mechanism of reducing the global total."
He indicated that paying for emission permits in the ETS might add €1-€2 (70p-£1.40) to the cost of an average flight ticket. Although environmental campaigners say the increase would be too small to have any effect on reining back the growth in passenger demand, Mr Sentence said: "Every price increase has an effect on demand."