Out of the total of 333 deaths, 87 people had been restrained, most commonly being physically held down by officers. In 16 of those cases, restraint was linked directly to the death, and four were classed as "positional asphyxia".
The majority were from natural causes, with nearly three-quarters relating to drug or alcohol abuse. The report questioned whether those arrested for being very inebriated should be taken to alternative facilities, such as the "drunk tanks" introduced in Scotland. It called on the Home Office and Department of Health to pilot facilities with medical care to replace police cells.
Those who died in custody were mostly white (75%), male (90%) and aged between 25 and 44.
The number of deaths each year had fallen from 49 in 1998-99 to 15 in 2008-09, slightly increasing to 17 last year.
Inquest, the independent organisation working to reform investigation into contentious deaths, said the findings were "depressingly familiar".
"The study points to alarming failures in the care of vulnerable detainees suffering from mental health, drug and alcohol problems, many of whom should have been diverted from police custody," said its co-director, Deborah Coles.
The report stated that fewer than half of detainees booked into custody who should have been risk assessed were actually assessed. Incidents where custody officers had not conducted proper checks, or thoroughly roused detainees to check their state, were "prevalent".
In many cases custody officers and staff lacked basic first aid training, it said.