SHAs' final act will be to oversee the transfer of public health from PCTs to local authorities, and of commissioning to GP consortia, the DoH has said.
At a debate held by the all party parliamentary group on primary care and public health, speakers highlighted the need for a smooth transition.
Kathryn Tyson, DoH director of international health and public health delivery, said SHAs were leading the process with their 'last gasp'.
It is SHAs' responsibility to log 'all the activity that is going on' and identify where services should be allocated, she said.
If this is unclear they should work through a process of 'best fit', Ms Tyson said.
A DoH spokesman said after the debate that 'any transition brings its own risks'. Therefore the process must be managed with oversight, he added.
'It's not all about transition; it is also about transformation,' he said. PCTs will also have a 'firm hold' on the transition process, and will remain in place until 2012, he added.
Nationally, Public Health England will play a role in overseeing the transfer of public health responsibilities to councils.
It will have a 'transition team' in place to ensure the changes are managed effectively, the DoH said.
David Stout, director of the NHS Confederation's PCT Network, agreed that SHAs were currently responsible for the 'overall running of the system' and therefore the current phase of transition.
But assuming the Health Bill proceeds as planned, it will be PCT clusters that have final transition responsibility, he argued.
PCTs will be 'there at the end' and although SHAs are currently responsible for the transition period, they will be abolished before the final transition from PCTs to consortia is complete, he said.