The financial crisis led to 5% fewer passengers using Britain’s leading airports in September than a year ago, intensifying the row over whether airports should be allowed to expand.

The government gave the go-ahead to expansion at two London airports despite the decline in traffic, but the Conservatives warned they would veto airport expansion plans if they win an election.

Airport operator BAA blamed the drop partly on the collapse of XL Airways last month, which led to a 12.6% fall in charter traffic to Europe across its airports and a 6.8% fall to North America and the Caribbean.

The biggest charter airport, Gatwick, suffered a 44% fall in transatlantic passengers and an 8.8% fall in European traffic.

But other airports and scheduled traffic were also hit by the downturn. Heathrow saw 3.6% fewer passengers despite a 9.6% increase in North Atlantic traffic chiefly due to airlines switching services from Gatwick. Passengers on European flights from Heathrow fell 8.1%.

Stansted saw a 4.7% drop in passengers, confirming a year-long slowdown at the biggest low-cost airport.

That did not stop the government agreeing a 40% increase in passengers at Stansted, from 25 million to 35 million a year, despite the objections of local authorities.

The government also gave the green light to expansion at London City, allowing a 50% increase to 120,000 take-offs and landings a year. Passenger numbers at London City are forecast to reach 3.2 million this year but remain static next year.

Conservative leaders warned BAA and its contractors to be “very careful” about expanding. Shadow transport secretary Theresa Villiers said: “I would advise them to drop it. We will not consider ourselves bound by any decision taken by this government. We do not want a second runway at Stansted.”

Industry leaders, including British Airways boss Willie Walsh, reacted with fury to Tory plans to veto Heathrow expansion when they were announced last month.

In Scotland, Glasgow airport was hit hard by the failure of XL Airways and Zoom Airlines and suffered an 11% fall in traffic compared with September 2007. Edinburgh saw a 2.9% fall and Aberdeen a 4.2% drop.

Airlines have announced wholesale reductions in services this winter, with some – including Ryanair – grounding aircraft rather than flying at a loss.