The commission confirmed it had received an official complaint, which was similar to issues raised in reports by Third Sector (7 November). These included how funds were used and allegations of bullying.
A YWCA spokeswoman said: "We welcome the opportunity to meet the large charities division of the Charity Commission to clarify the false allegations that have surfaced in Third Sector. We do not tolerate bullying and have a firm commitment to dealing with it if it ever surfaces."
The charity's accounts show it raised £816,000 in voluntary income but had £1.1m of fundraising costs in the financial year 2006/07.
The charity's operating deficits were covered by reserves. Last year, £2m (31 per cent) of YWCA's funding was from reserves, bringing the total sum of reserves spent since 2002 to £10m.
"We recognise and are committed to finding ways to increase our unrestricted income in what is a difficult funding environment for the charity sector as a whole," said the spokeswoman.
"YWCA has accrued a significant amount of reserves from the sale of housing stock and stock market gains. We feel it is inappropriate to sit on such a large sum and have committed to increasing the spending of reserves both on continuing to support our work with young women and investing in programmes to ensure our future growth as a robust, professional charity."
Shan Nicholas, the former chief executive of the Princess Royal Trust for Carers, started on Monday as interim chief executive of the YWCA.
She will take charge for the next six months while the search continues for a permanent replacement for Deborah Annetts, who left the organisation last month after only three months in post.
A spokeswoman for the trust said Nicholas left at short notice in September to pursue other career options.
She will be working with Christine Freshwater, who took over as YWCA chair three years ago and has been a trustee since 1999.
Freshwater, a former managing partner of accountancy firm Chantry Vellacott, took over when the YWCA began a drive to be seen as the leading young women's charity in England and Wales.