The eight regional forces, which are being merged from April 1, have different approaches to risk management, staffing and healthcare, according to a report by HM Inspectorate of Constabulary for Scotland.
The way custody suites are designed and managed also differs.
In one location, there was no female officer despite there being female prisoners.
One force had no dedicated custody sergeant and the ratio of staff to prisoners "varied widely" across the country.
Aberdeen was singled out for having a "high-risk" approach. The lack of call buttons in cells mean staff make checks every half- hour.
Money has been approved to deliver a new custody facility in the city but the report recommended an interim solution should be found.
About 170 detainees were seen during a series of unannounced weekend inspections in each of the force areas.
The HM Inspector of Constabulary in Scotland, Andrew Laing, said: "What this inspection shows us is people detained in police custody in Scotland are treated with dignity and respect by professional staff, and they have their care and welfare needs met.
"Against this positive picture there are a number of differences in approach between the current eight forces which will present the new single service with some challenges along with significant opportunities for standardisation, and the benefit that brings.
"That will include standardising the approach to risk management, staffing models, training and the provision of healthcare, and computer-based custody management systems."