The commission has launched a consultation on the new assessment. A spokesman said 'engagement of the health sector is absolutely crucial because area assessment is going to be a much bigger beast in its remit'.
He added that the commission was worried about a lack of health sector awareness of the new style of assessments.
A new framework will check the progress of primary care trusts and local government on their joint strategic needs assessment, which should focus on reducing health inequalities and promoting health and well-being.
The framework will also help determine priorities for local area agreements.
The role of local strategic partnerships between the NHS and local government in addressing the priorities identified in local area agreements will also be scrutinised as part of the new comprehensive area assessments.
The Audit Commission has organised a series of events in June to consult with the NHS on the future shape of the assessments.