The programme was originally mooted for roll-out in England in April 2007. But a DoH spokeswoman told GP it has decided that screening for CVD 'isn't very effective'.
GPs warned that this could leave some patients at risk.
Instead, a risk assessment and management strategy for CHD is being developed to be built into standard practice.
DoH heart disease czar Professor Roger Boyle said: 'We are developing a vascular strategy to look at risk factors that will build on the work that's already been going on, but bringing all cardiovascular diseases together.
'It's key work for primary care and they'll be involved in developing this strategy,' he added.
Rather than screening, the DoH is looking at 'improving public awareness of healthy living', said Professor Boyle.
'That's part and parcel of the process of life checks, which is already being developed across the country.'
Wigan GP Dr Mike Knapton, director of prevention and care at the British Heart Foundation, said: 'Simply doing risk assessment is not the same thing as screening.'
Risk assessment will fail to identify people at high cardiovascular risk who do not see their GP, he warned: 'That will then increase inequalities.'
North Yorkshire GP Dr Terry McCormack, chairman of the Primary Care Cardiovascular Society, said: 'It's a step backwards because screening doesn't happen at the moment and it's not going to happen without support from the government.'
GPs would welcome screening if it targeted those at risk, such as the over-45s who are obese, Asian or have a family history of CVD, added Dr McCormack.
In February, the Scottish Intercollegiate Guideline Network (SIGN) said all over-40s should be screened for CHD and stroke.
The latest move by the DoH could give England a time lag disadvantage for CVD screening.
But RCGP vice chairman Dr Graham Archard said a revision of the assessment method was better than rolling out an ineffective screening tool.
'If the DoH has evidence that a screening programme isn't effective it would be foolhardy to increase the pressure GPs and their teams are already under.'
April 2006: Diabetes UK conference told cardiovascular screening tool kit could be rolled out April 2007.
February 2007: SIGN issue guidelines on CHD and stroke screening for Scotland.
June 2007: DoH says tool kit to be replaced by risk assessment and management strategy.
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