An NHS headcount carried out by the Information Centre for health and social care has highlighted 9,858 duplicate entries.
The news will fuel criticism of the government's workforce data, which was lambasted in a health select committee report in March.
The report found that a lack of accurate information and forecasting had resulted in staff numbers rising above targets by up to 340 per cent.
.Health minister Lord Hunt said: 'The NHS traditionally never knew how many people it employed.
'What has been happening in the past few years has been a much more rigorous approach.
'The fact that they have identified these duplicates shows this is working and we expect to see even more analysis of the figures.'
The duplicate records are for 3,370 nurse full-time equivalents; 2,719 clinical support staff such as nursing assistants, medical secretaries and healthcare assistants; 1,818 scientific, therapeutic and technical staff; 1,562 infrastructure support staff from finance, IT and human resources; and 389 others.
Affected workers, who include nurses who hold family planning clinics, have not been paid twice, Lord Hunt emphasised.
The figures also revealed a small decline in the overall workforce for the first time since 1996.
The number of managers dropped by 2,600 to just under 37,000, and managers now represent less than 3 per cent of the total NHS workforce.