But the data still means that over 600 complaints are made every week.
Around one in five was related to rudeness by officers.
Claims by members of the public that they were sexually assaulted by police went up 30% in a year - and there was a similar rise in allegations of corrupt practice.
Freshly-released data from the 2006/7 British Crime Survey disclosed that over a quarter of those polled said contact with officers had left them "really annoyed".
But of those, just one in 10 made a complaint.
IPCC chairman Nick Hardwick said work to address complaints by forces could have a "positive impact".
He added: "The public recognise the police have a difficult job to do. However, this does not alter the fact that they expect officers to do their job politely and efficiently.
"These statistics show that when it is not done in this manner they are likely to complain."
However, Simon Reed, vice-chairman of the Police Federation, which represents officers, said it was important to look beyond the headline figures.
He said: "These complaints not only reflect the increasing pressures on police officers but also highlight the need to invest in appropriate training for officers so they have the confidence and skills to deal with the challenging situations they face.
"Despite many of these initial complaints not being upheld or proven, these statistics demonstrate that some forces are not learning lessons and those systemic and structural faults which hinder policing need to be addressed.
"It needs to also be borne in mind that the very nature of policing means that often police officers are interacting with those who would rather not be stopped or questioned by police and there is therefore an element of malicious complaints, which explains the high percentage of complaints that are unfounded."
Acpo spokesman Chief Constable John Feavyour said forces had worked hard to build confidence in the complaints process.
He added: "Each day, thousands of interactions take place with the public. Inevitably there will be occasions where we do not always get it right.
"When we get it wrong we should recognise the facts quickly, encourage debate and be willing to listen to the views of those who wish to engage in the policing debate and learn more from them."
The figures relate to 43 regional forces in England and Wales and the British Transport Police.
Individual complaints are broken down into component allegations.
In 2008/9 there were some 53,534 separate allegations, up from 48,280 the previous year.
Complaints about stop and search rose 27%, although the total numbered only 680.
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