In total, 6,000 children and young people said they have felt lonely or bullied at school.
"This is a big social problem and not enough is being done to put things right," Friends president Lars Arrhenius told Swedish Television News.
At the same time, one in three teachers said they did not know of any pupil in their school who had been bullied by another pupil over the past year. Every other pupil from age 12 and up reported feeling that members of staff are bad at intervening when they notice someone being mistreated.
"If we would see the kinds of things these pupils are talking about at work places, there would be much stronger reactions," said Arrhenius.
He added that he was not surprised by the findings since the situation in Swedish schools has been similar for a long time.
Seven per cent of survey respondents also claimed they had felt violated by a member of staff over the past year.
"It can be verbal. Perhaps one talks to the pupil in a condescending way or a pupil may be told they're not intelligent enough," said Arrhenius.