More than half of parents have concerns about bullying at school, rising to three-quarters of those with disabled children.
And a similar proportion are worried about their offspring's academic progress, claims a report to be published on Monday by the charity Children in Wales.
But most parents say they find their school approachable and it gives them enough information.
The survey, of 384 parents and 109 governors, found 64 per cent of parents always found it easy to approach their child's school.
But around half had concerns about bullying, academic progress, homework and poor behaviour. And nearly half were not formally involved in their child's school.
In all areas, parents of disabled children were least satisfied. For example, more than 75 per cent were worried about bullying and less than 30 per cent found their school approachable.
Tony Ivens, Children in Wales's fatherhood development officer, said he had been surprised by how negative the responses of these parents were, and that more research was needed.
"They are the most unhappy with schools, particularly in mainstream," he said.
The report says the findings on bullying are particularly worrying as they reflect concerns already expressed by children and disabled children.
"Parents need to know schools take the issue seriously and act accordingly," it says.
Schools should record bullying incidents involving disabled children in the same way as happens with racially motivated incidents. And the Assembly government should ensure all schools have clear and enforced anti-bullying policies, it recommends.
An Assembly government-funded study of anti-bullying polices in Wales, published in April, found a third were not up to scratch. Children's commissioner Peter Clarke said the findings confirmed his own concerns. His office is reviewing the problem with children, and hopes to report back by the end of 2007.
"I would like to see a child's complaint about bullying recorded as a formal complaint, to make sure that someone takes responsibility," he said.
"There is a mixed picture across the country. Some schools take ownership of bullying, they have peer support and other things to help prevent it, and remedies when it does break out.
"But occasionally you still get heads claiming they don't have bullying in their school."
Gareth Jones, director of the Association of School and College Leaders Cymru, said schools were already required to record bullying incidents.
"It is disappointing that the authors seem unaware of the existing legal requirements on bullying policies and the recording of incidents, let alone the existing monitoring by the Assembly government and Estyn of their effectiveness."
He added: "The fact that most parents are pleased and supportive of the efforts of their child's school is a cause for celebration."
Other research findings confirm that mothers do most of the home-school liaison, with fathers making up only 13 per cent of respondents. And it suggests parents are more geared up to 21st century technology than schools might think.
When asked how they preferred to be contacted, they rejected the traditional pupil post system and put text messaging first, followed by emailwebsite, then coffee mornings and newsletters.
'Parents and schools: making the connection, Children in Wales' tel: 029 2034 2434