Diabetes UK said government figures suggested around 9,500 people with undetected type 2 diabetes missed out on a diagnosis in 2011/12 because PCTs were too slow to organise checks locally.
In a report on the failings, the charity called on the government to ensure the transfer of responsibility for health checks to local authorities in April 2013 does not further damage the programme.
Diabetes UK's findings come after a GP investigation found a fifth of PCTs are set to fail DH targets for NHS health checks in 2012/13.
The NHS Health Check programme began in 2008 and aims to screen 15m people aged 40-74 for risk of heart disease, diabetes, kidney disease and stroke by 2018.
PCTs were given three years to begin a phased roll-out before the programme launched in April 2012. This included offering checks to 18% of the eligible population in 2011/12.
However, DH figures show over half (58%) of PCTs missed this 18% target. This means only three-quarters of all the intended health checks have been offered to patients. Uptake among those who were offered a check was low at just 52%.
NHS Milton Keynes, NHS Sheffield and NHS Western Cheshire did not offer a single health check in this year. A total of seven PCTs offered checks to less than 1% of their population.
Barbara Young, chief executive of Diabetes UK, said the poor implementation of the NHS Health Check scheme was a 'tragic failure' that had 'potentially dire consequences for the state of diabetes care in this country'.
She added: 'It is vital that people with type 2 diabetes are diagnosed as early as possible to reduce their risk of developing complications and we are concerned that the estimated 9,500 people who missed being diagnosed last year are at increased risk of amputation, blindness, kidney failure and stroke.'
The charity wants the new body Public Health England, which will replace the Health Protection Agency in April, to establish a national implementation plan for the scheme.