The commission refused to rule out redundancies after about 350 employees at its London, Liverpool, Taunton and Newport offices went on a one-day strike last week. The Liverpool premises were forced to close for the day as a result.
The Public and Commercial Services Union organised the action, which involved civil and public servants from 200 government organisations, in response to fears that Treasury cuts next year could lead to compulsory redundancies.
The Treasury is expected to announce the commission's next three-year funding deal in about a month's time. The last settlement, which occurred in 2004, saw the Government freeze the regulator's budget at £31.6m, which amounted to a 2.5 per cent fall per year in real terms.
Staff levels subsequently fell by 13 per cent to 517 in 2005/06. With the Chancellor warning small government departments to brace themselves for a 5 per cent budget cut from 2008, further job losses are possible.
"I don't think any employer in the public sector can rule out redundancies," said Nick Allaway, director of charity information and corporate services at the commission.
Allaway said the commission had no plans to make redundancies and had coped with the current funding freeze through natural wastage and voluntary redundancies. "We have never made anyone compulsorily redundant," he said.
But he warned that a reduction in funding could delay the commission's implementation plan for the Charities Act. "We have an expanding agenda and things that we want to do as a result of the act, so we are obviously trying to achieve a favourable funding settlement," he said.
The PCS followed the strike with a two-week overtime ban. It has called for the Government to issue a guarantee against further job losses.
Darren Jones, PCS branch secretary for the Charity Commission in Liverpool, said: "It is clear the commission will be expected to adhere to any cuts."
Jones added that pay levels at the commission compared badly with those of other members of the civil service.
In a statement, the commission said it had "offered a competitive pay settlement for the next two years".