Fresh fears about the dangers of the radioactivity contaminating a Scottish coastal resort have been revealed in hundreds of internal government emails obtained by the Sunday Herald.

Contaminated shellfish from Dalgety Bay in Fife have been officially deemed unfit to eat, while a UK government health watchdog has been accused by one of its leading advisers of downplaying the public health risks from the pollution.

The revelations will be raised by the former prime minister and local MP, Gordon Brown, at a meeting with the Defence Secretary, Philip Hammond, in London tomorrow. They emerge as discussions on how to clean up the contamination, blamed on old military planes, come to a head in talks this week.

The Sunday Herald understands that a plan to investigate the contamination until May 2013 is likely to go ahead. But it is still unclear how or when the area will subsequently be cleaned up, as the Ministry of Defence (MoD) is refusing to accept liability.

The Scottish Environment Protection Agency (Sepa) will therefore not lift its threat to formally designate Dalgety Bay as Britain's first radioactively contaminated land if the site is not cleaned up. But it is unlikely to implement the threat in the near future.

Contamination was first discovered at Dalgety Bay in 1990. It is thought to come from the radium used to illuminate the dials of aircraft disposed of in the area after the Second World War.

More than 2500 radioactive hotspots have been found on the foreshore, ranging in size from tiny specks to lumps as big as half-bricks. About a third have been uncovered since last September, including some of the most lethal ever found on public beaches.

The emails, released by the UK Health Protection Agency and the MoD under freedom of information law, shed new light on the arguments that have gone on behind the scenes in recent months about the dangers at Dalgety Bay.

One email, dated February 17, 2012, contains details of an initial assessment of the health risks of eating contaminated shellfish from the bay carried out by the government's Food Standards Agency (FSA). It concluded that the resulting radiation doses "could be potentially unacceptable".

Depending on the assumptions made, up to three-quarters of the particles found on the beach would give radiation doses in excess of the public safety limit if they were eaten in shellfish, the assessment found. Doses to young children could reach more than 50 times the safety limit.

The FSA said on Friday its assessment was being reviewed before it determined whether further controls on eating shellfish were needed. Members of the public are currently warned "not to consume shellfish gathered in the area".

Public advice from the Health Protection Agency (HPA) that risks from the contamination were "low" was criticised by Professor Alex Elliott from the University of Glasgow, the chairman of the government's advisory Committee on the Medical Aspects of Radiation in the Environment (COMARE). The HPA advice was "debatable", he said in an email on November 19.

He pointed out that there was no doubt that contamination as radioactive as that found at Dalgety Bay could damage the health of people who came into contact with it. He made suggestions for strengthening the wording of the HPA's advice that were ignored.

On Friday, Elliott confirmed that there was a "difference of opinion" between himself and the HPA, which was likely to be reflected in advice COMARE would be offering ministers. Too little was known about the probability of people being exposed to the contamination to be sure the risks were low, he said.

In an email on November 9, the HPA expressed concern about being "pushed" into making statements about health risks by a "press frenzy". In another email, the HPA was complimented on its "low-key line" by an official from the UK Department of Health.

Gordon Brown will attend a public meeting about the contamination organised by Sepa at Dalgety Bay primary school on Tuesday night.

He said: "I will be asking for a timetable for a clean-up plan for the area to be implemented.

"We need not only a plan for continuous monitoring but a plan for the removal of radioactive particles, and either a sea wall or other remedial work to prevent particles causing safety fears again."

According to Sepa's radiation specialist, Dr Paul Dale, it was impossible to be certain about the health risks because no-one knew how much radioactivity was contaminating the bay. The MoD had submitted a plan for investigating the site but Sepa was seeking clarification on "essential elements" before accepting it, he said.

Sepa declined to say what the MoD plan contained or whether it was likely to adopt it. The plan is due to be discussed at a meeting of local stakeholders on Tuesday. Dale will also be presenting evidence on Dalgety Bay to a COMARE meeting in London on Wednesday.

The HPA defended its health advice, insisting that it was not aware of any reason to alter it. A spokesman said: "We have complete confidence in our own assessment of the risks involved."

The MoD said it had demonstrated a "serious commitment" to helping Sepa with Dalgety Bay.

A spokesman said: "MoD has assisted Sepa voluntarily and we have reached agreement on the way forward, working together to assess residual risks and determine the scope of any remedial action."