The Government was last night accused of a cover-up over the safety of its mass meningitis immunisation programme after The Observer obtained confidential documents that show at least 11 people have died after injections to prevent the disease.

Although doctors have reported the deaths as part of routine monitoring of effects of the vaccine to the Medicines Control Agency (MCA), the Government has not published the figures and last night insisted the programme was safe.

Documents from the MCA obtained by The Observer show that since the immunisation programme began last year there have been more than 16,000 adverse reactions reported by GPs under the so-called Yellow Card system. The Department of Health estimates only 10-15 per cent of reactions are reported under the scheme so the real figure is likely to be far higher.

Britain is the first European country to introduce the vaccine. Although GPs have been told it cannot induce symptoms of meningitis, two of the deaths after vaccination have been attributed to 'septicaemia meningicoccal', the infection of the blood that results from the disease.

Each year around 1,500 people contract meningitis C, with about 150 fatalities. The Government has said the programme had reduced cases by 70 per cent since it was introduced last year. So far 13 million babies, children and adults have been immunised.

Shadow Health Secretary Liam Fox last night called on the Government to launch an inquiry into meningitis C immunisation, which was rushed in because of an expected rise in cases over the winter. 'If information has been withheld, it will lead to suspicions that officials have not been entirely frank. If 11 deaths have not been made public, the Government risks the public losing faith in the system. This is woefully incompetent.'

Fox, a GP himself, added: 'Immunisation is about a balance of risks. Although the balance is almost always in favour of immunisation, without information parents cannot be expected to make an informed decision.'

A Department of Health spokeswoman said it chose not to make the deaths public for fear of panicking parents into withdrawing their children from inoculation. The Medicines Control Agency had investigated all the deaths and decided there was no evidence of a link to the vaccines. 'We maintain the vaccine is safe,' she said last night.

A report from the Government's Committee on the Safety of Medicines last Thursday gave the vaccine the all-clear after extensive inquiries into the level of reactions. The main supplier of the drug, US company Wyeth, said it had not been informed of any fatalities by the Department of Health. Spokesman Don Barrett said: 'We are always in contact with the Department and the rate of reactions is considered to be at a very low level for the number vaccinated.'

Isabella Thomas, of vaccination support group Jabs (Justice Awareness Basic Support), said she had had reports of children having fits after being given the vaccine: 'I am not convinced by government reassurances. We are receiving daily calls from parents whose children have had serious reactions. We believe the Government introduced it far too quickly.'

Dr Jayne Donegan, a London GP who has seen an increase in reactions among children at her surgery, spoke of a campaign, encouraged by the Government, to brand people who do not have their children vaccinated as irresponsible. 'This is not necessarily true, especially with something as untried as the meningitis C vaccine.'

Adam Finn, a paediatric expert at Sheffield Children's Hospital who is carrying out trials of the vaccine, said he believed the drug was safe, although it had induced extreme reactions in some children. 'We don't want children having fits as a result of a drug that hasn't been properly tested, but equally we wouldn't want a perfectly good drug maligned on the basis of hearsay.'

He said the normal trials on a new vaccine were not possible in Britain because of the relatively small numbers of people who contracted the disease. Instead scientists had tested whether the vaccine produced sufficient antibodies.

He said the Government had a duty to give the public all relevant information about the drug: 'The public has sufficient intelligence to make the decision for themselves. The way to get them to accept it is to tell the whole story.'

Liberal Democrat health spokesman Euan Harris said he had already raised questions in Parliament about the vaccine. 'I am very pro-vaccinations,' he said, 'but I have been concerned about this.'