Around 3,500 NHS managers were told over Christmas that they are at risk of redundancy, HSJ has learned.

Although estimates shared with HSJ suggest there are 5,000 to 7,000 vacancies left in the system, it is thought unlikely that all those at risk of redundancy will get jobs with new organisations. Around 600 redundancies have already been made during 2012-13, with a worst case scenario of 4,000 lay-offs taking place this year.

Staff in primary care trusts and strategic health authorities whose functions are transferring to new bodies in April were supposed to receive a letter by the end of 2012 saying whether they are at risk.

Of the 3,500 staff identified as being at risk, 1,000 are in SHAs, with the rest in PCTs.

However some of those receiving “at risk” notices have also been told that they have got a job in the new system, while HSJ heard from one manager who had not received formal notification either way.

A job matching process, designed to determine which roles would directly transfer to new organisations, was due to be completed by the end of 2012.

Senior figures believe that many staff whose roles have not been matched to posts in the new system will still find jobs through competitions for the remaining posts.

Sir Neil McKay, the senior responsible officer for the human resources transition, told HSJ last month: “On one level it looks theoretically possible for everyone to get a job, but in practice we know that is not the case. Some people won’t have the skills necessary for a particular job, or there might be a geographical mismatch.”

However, he was “absolutely certain” that some people told they were at risk in December would still find jobs.

Sir Neil estimated that “more than half” of the jobs in the new system would be filled through the job matching process.

He said natural wastage and voluntary redundancy schemes had cut the numbers of staff affected by the transition to below the level of jobs expected from April 2013 – estimated at around 48,000 to 50,000.

HSJ understands that hundreds of staff assigned roles in new organisations are raising concerns over the new roles, where it is still not clear what the hours, locations or responsibilities will be, or where it appears that they do not match the skills or requirements of existing staff.

Those cases could progress to legal challenges or tribunals over the coming months if they are not resolved satisfactorily.

Jon Restell, chief executive of Managers in Partnership, said: “To date there’s been no active process of trying to redeploy at risk staff into jobs.

“If [the DH’s transition team] are serious about avoiding redundancies they need to spend the next four to six weeks identifying jobs that people could do locally, and where there are issues around skills they would be able to offer people training and redeployment.”