A £500,000 public dialogue over GM food could be abandoned after a second member of the steering group overseeing it resigned, the government's independent food watchdog said today.

The Food Standards Agency, which had been commissioned by the Labour government to gauge the public mood on growing and eating the controversial foods, said that it would ask the coalition government if it should continue with the dialogue.

"There has been a major change in government," said Nathalie Golden, a spokeswoman for the FSA.

"It will need to be presented to ministers. It depends on the new government whether it goes ahead."

Professor Brian Wynne, the vice-chair of the 11-person steering group, today became the second member to resign in the past eight days.

Wynne, an academic specialist on public engagement with science, said in a letter to the group that the planned consultation was biased in favour of the technology and was little more than propaganda for the industry.

He accused the FSA of having adopted a "dogmatically entrenched" pro-GM position and said that the dialogue could become a "public mistrust generator".

He was also heavily critical of FSA chair, ex-Labour minister Lord Rooker, who has described the public's sceptical position on GM food and crops as "anti-science".

His resignation follows that of Dr Helen Wallace, director of the thinktank GeneWatch UK who resigned last week in protest at the FSA's links with the agri-chemical industry which has been lobbying strongly to allow GM foods to be used more widely.

She alleged that some of the contractors being considered to run the project were already working for a major biotechnology company in order to "position the company as a positive force".

"It has now become clear to me that the process that the FSA has in mind is nothing more than a PR exercise on behalf of the GM industry," she said.

"In my view, this would be a significant waste of £500,000 of taxpayers' money. A process that was barely credible has become a farce.

"Taxpayers' money should not be wasted on a PR exercise for the GM industry."

Pete Riley, director of GM Freeze, a coalition of environment groups opposed to GM foods, said: "The GM public dialogue is now in chaos.

"The coalition government needs to look very seriously at how the FSA is attempting to use the dialogue process to gather information on what the public thinks about GM so they can the use it to manipulate public opinion in a pro-GM direction.

"This would be a gross misuse of public funds, and ministers need to put a stop to it.

"The FSA is far too close to industry on this issue, which is a deep disappointment for an organisation that was set up as an independent regulator and food safety champion for the public just 10 years ago."

But Golden said there were are no plans to delay the dialogue because of the resignations.

"The steering group is now in the process of identifying an organisation which might carry out the dialogue," she said.

"Once the steering group is in a position to suggest a body to do this, it will make a recommendation to the FSA board.

"The board will then ask ministers, before contracts are signed, whether the GM dialogue should proceed.

"The agency is completely independent. It is not at all a front for industry. We will all be considering the implications of these resignations."