The BBC Trust said it was "disappointed" by the time it took the corporation to deal with complaints after it ran its own mystery shopper investigation.
The BBC aims to reply to an initial complaint within 10 working days but researchers found almost half (44%) of emailed complaints were not responded to in that time.
A response to the findings from the BBC executive said the results were "disappointing but not entirely surprising".
It said the exercise was carried out at a time the corporation was experiencing "large volumes of audience complaints" with more than 13,000 complaints received about EastEnders, which was in the middle of a controversial baby swap plotline.
In 2010/11 the BBC received 240,000 complaints with almost three-quarters (74%) by email, 23% by phone and 3% by letter.
The mystery shopper study, which focused on 498 complaints, initially found 31% of letters received a response within 10 working days, but later updated that figure to 64% after postal delays were taken into consideration.
Every complaint by phone was answered and received a response.
The report said: "The trust is disappointed that the turnaround time for letters and emails was significantly lower than might have been anticipated in January 2011.
"The trust is reassured that turnaround times have recently recovered but regrets that some audience members would have experienced poor complaints handling during this period."
It also announced it would repeat the mystery shopper exercise.
Trust chairman Lord Patten recently announced the BBC was appointing a chief complaints editor, reporting directly to director general Mark Thompson, in a bid to make the process "as fast and effective as possible".
Trust member Alison Hastings said: "It's essential that the BBC handles complaints efficiently and well.
"The work published today shows that further progress is needed to ensure licence fee payers' complaints are being responded to in a consistent and timely manner."
A BBC spokeswoman said: "We welcome any report that helps us to improve our complaints service to audiences as we work hard to ensure that we listen to and respond to their feedback quickly, seriously and comprehensively. We are already implementing a new action plan to deal with the trust's findings."