There was a 40 per cent decline in the number of complaints dealt with by the commission in the past year, Berg's annual report reveals.
The number of unresolved complaints against the commission that were referred to the independent complaints reviewer also fell from 110 in 2004/05 to 104 in 2005/06.
But there was a fourfold increase in serious complaints that were unresolved by both the commission and the independent complaints reviewer and had to be referred to the Parliamentary Ombudsman. Serious complaints rose from one in 2004/05 to four in 2005/06.
Complaints about the time the commission took to deal with a complaint were also up by a third.
Jonathan Brinsden, charity lawyer at Bircham Dyson Bell, said that the predominantly positive report belies the fact that people still face many everyday problems that they do not want to waste time complaining about.
"It takes an awful lot of time to get a response out of them," Brinsden said. "They also have a staff turnover like you wouldn't believe. It's a growing industry, but the infrastructure has not grown with it."
The commission has launched a major review of its customer complaints procedures, which is due to report in October.
It is hoping that this will motivate many charities to follow suit.
The Charities Bill will also give charities the opportunity to air their grievances through a new Charity Appeal Tribunal.
The commission's annual review found that it had improved its recording of compliments, with 922 received in 2005/06. This was a significant increase on the 547 recorded in the previous year.
The majority of the complaints received related to the commission's perceived lack of responsiveness to allegations against charities.