A major study of illegal exclusions by children's charities SNAP Cymru and Barnardo's Cymru reported that schools often use the practice to ease difficult situations and relieve pressure on teachers.
Researchers found that some pupils were asked to stay at home during events such as trips, inspections, photo days, concerts and plays, because staff could not provide behaviour support on "non-routine" school days.
The groundbreaking National Behaviour and Attendance Review (NBAR) in Wales called for an end to unofficial exclusions in 2008. It said the practice was seen by some pupils as a "reward" for bad behaviour and gave them unwarranted kudos among their peers.
In 2009, the two children's charities put pressure on the Welsh Government to commission further research into the practice, amid fears it was behind a drop in official exclusion statistics.
SNAP and Barnardo's studied the experiences of 52 primary and secondary pupils who had been illegally excluded at least once, interviewing their parents as well as 15 education professionals with expertise in exclusion.
The researchers found that illegal exclusions still occur in schools despite "strenuous efforts" by local authorities to prevent them.
Some educationalists told the researchers that illegal exclusions were considered to be in the best interests of schools because they left no statistical record and kept their official exclusion figures low.
Two heads said the practice was explained as pupils "needing time off" without an official exclusion being on the school record.
The professionals disagreed on whether illegal exclusions worked; some thought they offered a warning while others felt they were ineffective and denied rights.
But the parents unanimously felt that schools were using illegal exclusions in an effort to manage behaviour, and said they had a negative impact on their children's educational and emotional wellbeing.
Among the report's 27 recommendations were more preventative measures and improved communication with parents.
It also said schools should have more "flexible options" for offering support because illegal exclusions often occur when they do not know what other action to take.
NBAR chairman Professor Ken Reid said it was "disappointing" that the report highlighted similar concerns to those of his own group.
He said: "It suggests that some of the core recommendations and changes which NBAR suggested needed to be implemented in the ways in which exclusions are managed in Wales have been broadly ignored over the last three years.
"It is difficult to understand why, as NBAR's recommendations were based on extensive consultation."
The Welsh Government said it commissioned the research in a bid to improve approaches to managing behaviour in schools and ensuring that exclusion processes are used "lawfully and responsibly".
A spokesman said: "We will draw on this research as we implement our new behaviour and attendance action plan."