Thousands of passengers from all over the world arriving on private jets were allowed into Britain this summer without any passport checks as a matter of official policy, according to leaked UK Border Agency emails.

The internal reports show that immigration and customs staff were instructed not to meet passengers on private charter flights, including executive jets, as part of the "light touch" targeted approach secretly adopted this summer.

The emails also reveal the extent that full passport checks on European passengers were scaled back under the "limited pilot scheme" authorised by the home secretary, Theresa May, on 28 July.

The level 2 checks, which suspended the checks on biometric passports of EU travellers, were used hundreds of times each week during the summer.

May said on Monday night, in reply to 14 questions posed last week by Keith Vaz, the Commons home affairs committee chairman, that the "limited" pilot scheme had in fact applied to all ports and airports in Britain. The 'lighter touch' checks were used at 28 ports and airports: Aberdeen, Belfast, Birmingham, Bournemouth, Bristol airport, Calais, Cardiff, Coquelles, East Midlands, Edinburgh, Exeter, Gatwick, Glasgow airport, Harwich, Heathrow, Leeds Bradford, Liverpool, London City, Luton, Manchester airport, Newcastle, Newhaven, Norwich, Plymouth, Poole, Portsmouth, Prestwick and Stansted. In the first week of the pilot the checks were relaxed on 100 occasions across the country. This rose to 260 occasions in week six of the pilot, and 165 in week nine, which ended on 9 October.

The emails show "lighter touch" checks were being used by UKBA local managers in "sharp bursts" to redeploy staff to high-priority targets such as suspected drug smugglers and clandestine entrants and to "mitigate pressure of excessive queues".

The disclosures come as the departed head of the UK border force, Brodie Clark, prepares to fight to clear his name and retain his pension when he appears before the Commons home affairs committee on Tuesday. He is expected to challenge the home secretary's claims to the Commons that he is to blame for the scandal by going beyond ministerial instructions.

The shadow home secretary, Yvette Cooper, said the leaked UKBA emails contained startling new information. "Last week the home secretary told us that no one had been waved through without checks this summer. But these documents show passengers on private flights weren't even seen. Last week the Home Office wouldn't admit to having figures about how often checks were downgraded. Now we know those figures exist, and that checks were downgraded 260 times in one week alone – potentially for hours at a time."

Cooper said the facts should be released immediately: "As long as she [May] refuses to do so, and keeps running away from media interviews, people will think she has something to hide."

The emails detail UKBA staff at Durham Tees Valley airport raising concern at a new policy of not being "allowed physically to see the passengers" arriving on private charter flights.

Although passenger details had been filed in advance, no passport checks were to be done on arrival nor checks against watchlists. "We've no way of checking whether the handling agent information is correct, or even if the number of people on the plane matches the number we've been advised," says the concerned official.

He says airport staff continued to feel uneasy at an instruction "at odds with national policy and is creating an unnecessary gap in border security which, if exploited by the unscrupulous, could bring the agency into disrepute".

In reply, the UKBA management told him the instruction was not against national policy but part of a new national general aviation strategy covering private flights which meant that arrivals did not have to be met. He was also told the policy was being implemented at many airports. The instruction to abandon the checks was dated 2 March 2011.

The UKBA staff protest that the "no checks" policy was "creating a situation where we are not able to secure the border as robustly as we would like to, for no justifiable reason".

The official response said it was appreciated that the move to the pre-clearance of private flights could "be perceived as a step down from meeting 100% of GA [general aviation] arrivals in Durham Tees Valley, but we are confident that through application of robust risk assessment and risk testing ... we are responding proportionately to the risk posed by general aviation".

The UKBA response also assured the staff there "will be no accusation of dereliction of duty as long as the procedures have been followed".

The reply adds that the term general aviation covers all flights other than military, scheduled and regular cargo flights. The Treasury estimates there are 80,000-90,000 private flights a year arriving in Britain.

A UKBA spokeswoman said: "It is not true that we don't carry out passport and warnings index checks on private flight passengers and will deploy officers to airfields where we have concerns."