The staff, all members of the professionals' union Prospect, are fighting the refusal of the Commission's Board to protect their pensions after they are transferred to the private sector. They work at the Commission's headquarters in London and at regional offices in Bolton, Bristol, Cambridge, Exeter, Gateshead, Leeds, Leicester, Lincoln and Solihull.
The Government last year announced it was closing down the Audit Commission by April 2013 and transferring its work to private sector providers. A number of staff are also trying to set up as a mutual and continue to offer a service to the Commission's public sector clients in the NHS and local government.
In negotiations with Prospect, Chief Executive Eugene Sullivan and the Board of the Commission have refused to apply the terms of the Fair Deal on pensions, the Cabinet Office agreement which protects the pensions of staff on transfer out of the public sector.
But when a Prospect delegation met Robert Neill, Communities and Local Government Minister, in October he confirmed there was no ministerial block by DCLG on the terms of the Fair Deal being applied to Commission staff.
Prospect negotiator Richard Hardy said: "The only thing standing between our members and a fair deal on pensions is the obstructive attitude of the Board and the Chief Executive, whose own pensions will not be at risk.
"Since they seem prepared to see our members stripped of their pension rights, we have no alternative but to raise the stakes and ballot on industrial action.
"We deeply regret having to take this action and call on the Chief Executive to think again and play fair by his staff before any clients are inconvenienced."
The ballot is authorised by Prospect's national executive committee. It is scheduled to start on 14 November and will close on 28 November.
The Audit Commission branch of Prospect intends to reopen negotiations as soon as the result is declared. The union is also taking legal advice over a potential judicial review of the Commission's decision not to implement the Fair Deal on pensions.
The Audit Commission audits £200bn of expenditure by public bodies in local government, health, housing, community safety and the fire and rescue services. More than 600 of its 2,000 staff have left employment since the closure was announced in August 2010.