A report by Diabetes UK found just 6.4% of people aged 40 to 74 attended a health check between April and December 2013, the nine months after the programme was handed to local government control.
A total of 11.25% were expected to have received the checks, which look for cardiovascular risk factors, in this time.
NHS Health Checks in Local Authorities showed the number of checks given in different regions widely varied, ranging from 0.3% in some areas to 23% in others. Only eight authorities managed to deliver checks to 11.25% or more of their eligible population.
The charity said very low acceptance rates in some areas ‘highlighted concerns’ that local authorities may not be offering the service to patients in an effective way.
Barbara Young, chief executive of Diabetes UK, said the checks had the potential to prevent thousands of type 2 diabetes cases.
She added that it was 'worrying that in some areas hardly anyone is getting one and in those areas it really need to be a priority to change this so that people get these checks wherever they live'.
Public Health England (PHE) has overall responsibility for the health check programme. Jamie Waterall, PHE lead for NHS Health Check, said: 'Local authorities are focusing on the important challenge of encouraging more people to have their NHS health check and we are working closely with them to offer support.'
The checks, offered by GP practices and some pharmacies, screen patients for their risk of heart disease, stroke, diabetes, kidney disease and certain types of dementia.
Last year, a GP survey found less than a quarter of GPs think the NHS should offer general health checks.