Delays were still expected at airports throughout the country despite a last minute block being placed on industrial action planned by BA cabin crew strike and an overhaul of aviation “no fly” rules to reduce future airspace closures caused by Iceland's Eyjafjoell volcano.
Officials on Tuesday admitted disruptions would likely continue for most of the week.
Airlines were struggling to return schedules to normal after plumes of thick ash drifted over the continent, closing major airports and leaving more than 1,000 flights cancelled.
Airlines, which have lost millions of pounds due to the ash alerts, condemned Monday's closure of airports and criticised the model used to predict the spread of the volcanic ash as "outdated and inappropriate".
Executives reacted with fury to what they argued were unnecessary restrictions introduced by overcautious safety watchdogs.
British Airways chief executive Willie Walsh led the criticism, labelling restrictions as "a gross overreaction to a very minor risk”.
Experts said the volcano, which last month caused much of Europe's airspace to be shut down for a week, has emitted massive amounts of ash, which can clog jet engines, since it began erupting a month ago and warned there was no end in sight.
Last month’s volcano eruption forced most countries in northern Europe to shut their airspace, grounding more than 100,000 flights and an estimated 10 million travellers worldwide.
The Air Transport Association (IATA), the international airline industry body, estimated that last month's shutdown – Europe's biggest since World War II – cost carriers more than £1.1 billion.
The latest eruption forced London’s Heathrow and Gatwick airports to shut for six hours on Monday, leading to hundreds of delays and scores of aircraft in the wrong place.
Nearly 200 flights were cancelled at Heathrow, 88 at Gatwick and 40 at Liverpool airport. Up to 50,000 passengers were affected.
Airport officials warned travellers it would take time for airlines to clear the backlog of delayed flights and advised them to contact their airlines before going to the airport.
After the day of chaos, passengers later received a double dose of good news after the High Court outlawed the back-to-back strikes by BA cabin crew while the Civil Aviation Authority (CAA) altered its criteria for permitting aircraft to fly.
The court ruling came too late for BA to reinstate its full flying schedule at Heathrow, which had been disrupted earlier in the day by the ash cloud.
Despite the High Court injunction, British Airways admitted that flights will still be affected for the rest of the week
The airline has been frantically trying to reinstate the 80 short haul and 30 long haul flights from Heathrow which faced cancellation had the strike gone ahead.
A spokesman for the airline said half of short-haul and 40 per cent of long-haul services from London’s would be affected because it is too late to reinstate a full service.
He added that its operation, however, was expected to return to normal by the weekend.
The ruling was a huge relief for the airline which told the court that the planned four five-day strikes would have cost the airline £138 million.
Unite, the union representing BA cabin crew, is preparing to appeal against an injunction which halted strike action planned by thousands of its members in the bitter row over jobs, pay and staffing levels.
The judgment came as the CAA announced that it had created a new “time limited zone” (TMZ) to allow certain aircraft to fly through a greater density of ash than previously permitted.
The change, which came into affect at midday on Tuesday, will only affect Flybe at first, but other airlines are expected to follow.
Once manufacturers and airlines have presented a joint “safety case” which proves they can fly through the ash without damage, they will be allowed to fly.
"As a result of this change, there are no predicted restrictions on UK airspace in the immediate future,” said Richard Deakin, the chief executive of Nats, the Air traffic control company.
The CAA appeared to blame the Met Office for the latest shutdown.
“The Met Office model was predicting ash which was not there when the test flights were done,” a CAA spokesman said.
“We have asked the Met Office why their forecast model showed something which was not subsequently backed up.”
The Met Office defended its computer model, insisting it was supported by satellite imagery, observation, laser checks of the dust in the atmosphere and other evidence from test flights.
It said the ash was present over the South East but not in the levels that ground aircraft
“The amount of ash is fluctuating on an hourly basis. The situation is very fluid,” a spokesman told the Daily Mail.
In Iceland meanwhile, there is no sign of the volcano stopping.
Experts said the Eyjafjoell eruptions, which began on April 14, have peaked three times, with the latest surge of activity coming Friday.
“Since the beginning of the eruption, we estimate that 250 million cubic metres (8.8 billion cubic feet) of tephra (ash and other fragmental material) has been produced," said Icelandic geophysicist Magnus Tumi Gudmundsson.
The Icelandic civil protection agency said the ash cloud was drifting to the north and was not expected to travel to Europe in the next two days.