The Independent Office for Police Conduct (IOPC) said an “overly complex” system means some forces are choosing to formally investigate most allegations, while others are going through a less formal process.
The body welcomed changes being introduced next year to standardise and simplify the complaint handling process across forces.
Regional Director Miranda Biddle said: “We hope the changes coming next year will make the system much more consistent and transparent which should help improve public confidence.
The decrease in the number of complaints recorded indicates that improvements are being made at local level and that the police are already adopting some of these changes when they deal with less serious complaints.”
The number of complaints made to forces in West Yorkshire, South Yorkshire and North Yorkshire all fell markedly in 2017/18.
Only Humberside Police saw the number rise by a fifth.
Complaint rates at forces are measured by the number of allegations logged per 1,000 employees, with the national average being 274.
Humberside Police had the highest complaint rate in the region, at 410 allegations per 1,000 employees.
Deputy Chief Constable Chris Rowley said: “In the figures quoted up to March this year, we were recording every single element of a complaint separately, which isn’t required and is an over recording.
“This is an indicator as to why the figures are significantly different when in comparison to other forces.
“We’ve now changed how we record and our own analysis over more recent months has seen us to be more in line with the national average.”
West Yorkshire Police’s rate was 278 and North Yorkshire Police’s rate was 201.
South Yorkshire Police had the lowest rate, at 176.
Detective Chief Superintendent Oz Khan, who leads West Yorkshire Police’s Professional Services Directorate, said: "We welcome the changes being introduced next year and look forward to working with our partners to implement these changes."
Maria Taylor, from the Professional Standards Department at North Yorkshire Police, said: "Taken as a whole, the report shows that North Yorkshire Police handles complaints well, but we need to do more to make sure our recording processes align with the national approach. We met with the IOPC to look into this two months ago, and changes are already under way.”
Deputy Chief Constable Mark Roberts, of South Yorkshire Police, said: “I welcome the reduction in both complaints and allegations against the force and I remain committed, with my colleagues, to continuing to improve the standard of service we deliver in South Yorkshire."