The investigation by the Centre for Research on Families and Relationships at Edinburgh University, along with ChildLine Scotland, undertook an in-depth investigation into 2,000 of 9,000 calls to ChildLine over four years.
Children of problem drinkers accounted for nearly a third of calls. In 40 per cent of those, children were calling because they were physically abused.
The researchers' report, published on Wednesday, said such problems were often hidden because young people felt unable to talk to adults about them.
One said: "I'd be worried about how my parents reacted."
Anne Houston, director of ChildLine Scotland, said: "Parental ill-health impacts directly on children, many of whom suffer serious problems in the home. Children have a clear insight into some of the causes of their problems and need to be listened to when services are being planned.
"They need more child-friendly protection services where they are the central focus. This is not about demonising parents. They, too, need support. Without support, the cycle of neglect and potential violence continues."
Kathleen Marshall, Children's Commissioner in Scotland, said: "We won't get workable solutions unless they build on what children and young people are telling us."
One youngster said: "Adults sometimes interfere without being asked and don't ask the child what they would like them to do."