Rooting about for Mediterranean holiday possibilities on the Expedia website recently, I came across a flight for £300. About half of that was the fare; the rest was labelled “taxes and fees”. I do not regard taxation as theft and I accept that air travellers should pay for the environmental damage they cause. Still, a 100 per cent tax rate did seem steep.

I carried on clicking and discovered I was getting off lightly. On the British Airways site, I investigated what tax I would pay if I were setting out this morning from London’s Heathrow to New York’s JFK. When I looked, an economy flight leaving this Tuesday and returning on Tuesday next week was selling for £296.40 ($583). The fare accounted for just £80 – which suggested a ticket tax of 270 per cent.

I asked BA to explain how this excess was calculated. It turned out that only £55.40 was straightforward taxation: £40 in UK air passenger duty and £15.40 in US arrival and departure taxes. There was also a US customs user fee. As passengers cannot say they would actually prefer not to use customs, I suppose this counts as a tax too, as does the US “immigration user fee”.

But there are also airport passenger charges (far higher at Heathrow than at JFK) and security charges. Biggest of all was a £126 fuel surcharge, which is not a tax at all.

Airlines object when governments load extra charges on to their tickets. They do not help themselves by making the tax component of their fares so opaque. But governments are to blame too: they should have come up with a uniform taxation system for this most international of industries rather than the existing hodgepodge of national charges.

The most obvious tax would be on aviation fuel. The problem is that tax on fuel for international flights is outlawed by the Chicago Convention, international aviation’s Magna Carta.

Most countries do not impose value added tax on international flights, which means the industry was for years undertaxed. The UK government set out to remedy this and has since become an enthusiastic taxer of air travel. As 20 per cent of international flights begin or end in the UK, the most important airlines have all been dragged into the net.

When the Conservative administration introduced air passenger duty in 1994, it did not pretend it was anything other than a way to fill government coffers. There was no mention of the environment.

As air passenger duty has climbed (it is now £80 on a business class flight to a non-European destination), the government has increasingly described it as a green tax, there to ensure the industry covers its environmental costs.

The airlines insist they more than cover them, which sounds fanciful, given that flying’s depredations extend beyond carbon dioxide emissions to noise and traffic congestion around airports. But a recent study by the independent Institute for Fiscal Studies says that, although the external costs of aviation are uncertain, studies indicate the airlines’ claim is broadly true.

Low-cost carriers such as EasyJet have objected that the duty does not focus on the real environmental offenders as it does not distinguish between flights on fuel-efficient aircraft and wasteful ones. Because all non-European destinations are subject to the same duty, passengers flying to New Zealand also pay no more than those travelling to Morocco.

The government has agreed that, from next year, taxes will be imposed per aircraft rather than per passenger. Its recent tax changes have been fiascos. Fortunately, it has asked for comments on this one as it looks like being a fiasco too.

The government says its favoured method of assessing the tax will be an aircraft’s weight at take-off combined with the distance travelled. As many in the industry have pointed out, this will provide no incentive to use more efficient aircraft.

It will also encourage airlines to use smaller aircraft, when the best environmental outcome would be to reduce the number of flights by using larger ones.

There is also the practical problem of how airlines will pass this tax on to customers. At present, each customer who flies pays duty. What would happen under the proposed system if the family in row 35 failed to show up and the airline found itself short of the money to pay the per-aircraft fee? Would the cabin crew organise a whip-round among the other passengers?

The European Union is proposing a different approach: capping airline emissions at the average level of 2004 to 2006 and issuing emission permits to carriers. A small proportion of permits would also be auctioned. Any airline that wanted to exceed its level would have to buy additional permits. This would force the industry to innovate to keep emissions down.

The problem is that the rest of the world does not want an airline emissions trading system. Given how chaotic and dysfunctional the existing airline tax systems are, the rest of the world should come up with a better idea if it can.