Former Labour cabinet minister Chris Smith has weighed into the row over controversial plans to expand London Heathrow criticising the government for trying to delay new pollution rules.

Environment secretary Hilary Benn has confirmed that Britain intends to seek a derogation from the European Union air quality directive for up to five years. Smith, a former culture secretary who is now chair of the Environment Agency, linked this to predictions that pollution at Heathrow will breach legally binding limits in the directive, due to come into force in 2010.

He asked: “How will the further expansion of Heathrow, and the inevitable and detrimental consequences on air quality and emissions, help in meeting a target that it is predicted we will exceed?”

Smith’s comments come as it emerges that senior minsters, including Benn, are opposed to Heathrow expansion. Transport Secretary Geoff Hoon had been expected to give the go-ahead for a third runway, to open in 2020, but it has been reported that the Cabinet is now deeply split on the issue. One source told newstatesman.com that supporters of the runway are increasingly isolated in the government.

Proposals put forward by the Department for Transport (DfT) would see increased flights from around 2012 through “mixed mode” operation – allowing take-off and landing on both runways at the same time. Ministers have acknowledged that expansion will only be possible if pollution limits in the directive are not breached around the airport.

But documents obtained by Greenpeace under the freedom of information rules show that the DfT predicted that levels of nitrogen dioxide at Heathrow will breach the directive in 2010. DfT officials subsequently worked with Mr Benn’s Defra department to ensure that negotiations over the directive “take account of Heathrow position”.

In a letter to Liberal Democrat transport spokesman Norman Baker, Mr Benn has confirmed that he expects to ask the European Commission to allow Britain to delay nitrogen dioxide limits, possibly until 2015. Mr Benn denied that anticipated breaches at Heathrow were the sole reason for this, although he did not deny that Britain could comply earlier than 2015 if it were not for Heathrow expansion. He told Mr Baker “The problem is one of existing pollution from traffic in London, including Heathrow, and in other major cities across the UK.”

Lord Smith signalled that the Environment Agency will continue to challenge the government over the directive. He said: “The government are entitled to ask for a derogation, but this does not come without strings attached. During the forthcoming Defra consultation on the new action plan required as part of the derogation process, the Environment Agency will remain vigilant as the watchdog for promoting environmental sustainability.”

The Environment Agency works to deliver the government’s air quality strategy in England and Wales. Earlier this year, it criticised the DfT’s Heathrow consultation, including claims that pollution could be reduced to comply with the directive after 2015.

In July a delegation of local authority leaders and MEPs asked EU environment commissioner Stavros Dimas not to allow Britain to stall on the directive. Green Party MEP Caroline Lucas said: "When I met Commissioner Dimas earlier this year to discuss Heathrow, he agreed that a UK request for derogation on the Directive would undermine the spirit of the targets set by the EU. Ultimately, what we need are clearer skies, cleaner air and a government which takes its responsibilities seriously by adhering to the EU legislation put in place to protect human health and the environment."

Lucas said it was “embarrassing” for a government that is attempting to position itself as a world leader on tackling climate change to be seeking a delay.