An EU deadline for lifting restrictions on carrying liquids onto aeroplanes by 2013 is under threat after the US government warned it will impose further security checks if there is a partial relaxation of the ban.

A planned change in liquids regulations for transfer passengers carrying duty free purchases on 29 April, viewed as a step change to a complete lifting of the ban in two years' time, was cancelled at the 11th hour after the US warned that it would introduce its own measures in response.

In an email to aviation bosses, a Brussels official said: "The US had informed the [European] Commission on 28 April that they would require additional measures for liquids to be taken on US-bound flights that were expected to cause great confusion for passengers at EU airports on whether or not they could take third country duty free liquids onto a connecting flight. The commission wanted to prevent such a situation."

Hours after receiving the warning from US officials, the EU announced that it was scrapping plans to allow transfer passengers on flights originating outside the EU to carry duty free purchases such as perfume and alcohol on to connecting services at European airports.

According to one industry insider, the US Department of Homeland Security was considering additional checks for passengers once they arrive in the US if the partial lifting of the ban had gone ahead.The email from Filip Cornelis, head of aviation security at the European Commission, added that a compromise was thrashed out with the US last month but that also fell down. "Unfortunately, a few days later it turned out that the 'agreement in principle' was not acceptable for Washington."

The 29 April move had already descended into confusion by the time Brussels announced its about-turn. The UK transport secretary, Philip Hammond, refused to lift restrictions for transfer passengers at British airports and was joined by his counterparts in France and Italy, while Germany and Scandinavia had prepared to implement the changes.

Aviation experts and politicians warned that the clash over a minor change to liquids regulations posed a threat to a complete lifting of the ban in April 2013 because if the US remains concerned it could impose a further wave of security restrictions in the wake of any relaxation, effectively negating EU changes. Chris Yates, an aviation analyst, said airports were also dragging their feet over investing in new technology that would allow screening of suspicious liquids, at a cost of up to £100,000 per machine.

"If the aviation industry has its way 2013 is probably in doubt," said Chris Yates, an aviation consultant.

The British chair of the European Parliament's transport committee also warned that the 2013 deadline could slip, with the US intervention bolstering airports' concerns. "I am worried about 2013," said MEP Brian Simpson. "For me it is not a security issue. It is a cost issue and that will still be there in 2013."

Current rules bar all passengers from carrying liquids on to planes unless they are in individual containers no bigger than 100ml. Introduced after police disrupted a plot to blow up airliners with liquid bombs in 2006, the ban has forced the confiscation of water bottles, shampoo and baby food at terminals across the continent. An aviation industry source said a wholesale lifting of liquid restrictions would require better technology and significant investment at hundreds of airports to install those machines. Until then, the source added, doubts will remain.

The head of the UK Airport Operators Association, Darren Caplan, warned that meeting the 2013 deadline should "in no way be at the expense of security effectiveness". He added: "Currently, the new technologies and processes required to screen liquids, aerosols and gels are simply not yet mature or adequately tested to the needs of a massive European aviation sector, catering for 1.5 billion passengers and 400 airports. Relaxing the ban in 2013 should not be about politics or cost – it should simply be about technology preparedness and delivering the highest levels of security for passengers."

Smiths Detection, a major supplier of airport X-ray machines, said more than 1,000 of its machines were deployed around the world and most needed only a software upgrade in order to detect suspect liquids.

A spokesperson for the DfT said the UK government remained "committed" to the 2013 deadline.

The email, seen by the Guardian, emerged as aviation security chiefs from EU member states prepare to meet this week to discuss the liquids ban, followed by a ministerial-level meeting later this month.