The draft strategy, seen by HSJ, which covers the years up to 2010-11, identifies claims for back pay as 'the biggest pay and workforce risk' ahead, and warns that 'uncertainty on a number of key legal issues' makes it difficult to assess the cost.'
It says that there are currently nearly 11,000 back-pay claims outstanding from lawyers acting on a no-win, no-fee basis, as well as trade unions representing NHS staff members, with the number rising by about 200 claims a month.
In the note on risk and obstacles to the workforce strategy, the workforce directorate said it expected the situation will 'become clearer' following a number of hearings on leading cases later this year.
Mike Jackson, Unison's lead negotiator on AfC, told HSJ that some back-pay claims had arisen because a number of clear cases of gender discrimination had come to light.
Last March, following a landmark case, North Cumbria Acute Hospitals trust agreed to pay 1,500 female staff arrears dating as far back as 1991 as part of an equal value settlement which it costed at£60m, and which predated the introduction of AfC.
'Under sex discrimination legislation staff can claim six years' worth of back pay. However, until Agenda for Change was implemented we did not reliably know where the discrimination existed,' said Mr Jackson.
He confirmed the DoH's predicted figures although he said that last October (a month after the DoH memo was written), 1,000 new claims had been lodged.
Mr Jackson said that if the claims were successful the government could be forced to pay out millions of pounds to NHS staff.
'Unison put a claim in to both NHS Employers and the DoH to settle the back-pay claims last year but they weren't interested in negotiating with us and that is when we started to lodge the claims at employment tribunals,' he said.
Mr Jackson said that he expected the first case for a back-pay claim under AfC to be heard at a tribunal in Newcastle in February.
NHS Employers head of pay Gill Bellord said the organisation was confident that AfC's job evaluation system would provide a defence against equal pay claims in the future. But she said the organisation was aware that a large number of retrospective equal pay claims were being lodged against trusts.
She advised: 'We know that employers have real concerns about the possible impact of equal pay claims and they should register claims with the NHS Litigation Authority in the first instance as a consistent approach to handling claims could help to minimise total costs to the NHS.'
In particular, Ms Bellord warned employers to think about the possible demands they would face in order to defend claims. 'We would advise employers to think about the possible demands on them in terms of administration and information collection that they will be expected to provide should they need to defend claims, for example in terms of reviewing payroll and personnel records,' she said.