Paula Lavis of YoungMinds said the true scale of self-harming could be far greater.
The figures were revealed in a study monitoring young people's wellbeing, which also showed smoking and drinking among teenagers is declining steadily.
The assembly government said the research will inform future policy.
The wide-ranging 2011 Children and Young People's Wellbeing Monitor for Wales is an attempt to pull together information on all aspects of children's lives.
Examining existing data on issues such as education, health and tackling poverty, and conducting surveys, it covers the lives of Welsh children from birth until the age of 25.'Tip of the iceberg'
Hospital admissions for self-harm in Wales have increased, particularly among 15-17-year-old girls, from approximately 650 incidents per 100,000 people in 2003-2005 to about 900 per 100,000 in 2006-2008.
Paula Lavis said: "These figures highlight how big an issue self-harming is among some young people.Continue reading the main story Between 1995 and 2008 cases of chlamydia among 15 to 24-year-olds increased from 192 to 758 per 100,000 populationHospital admissions for self-harm increased among 15 to 17-year-old girls - from approximately 650 incidents per 100,000 people in 2003-2005 to around 900 per 100,000 in 2006-2008.The number of babies born with foetal alcohol syndrome in Wales rose by 10% in 2009The number of live births in Wales increased from 32,000 in 2006 to 34,900 in 2009.Death rates among 0-19 year olds in Wales continue to fallThe infant mortality rate continues to fall and in 2009 was 4.8 per 1,000 births.In 2010 the proportion of pupils achieving at least level two in the Core Subject Indicator in the National Curriculum was 81.6% - the highest for 10 years.The numbers of young people not in education, employment or training (NEET) have remained at the same level for more than a decadeThe suicide rate for 15 to 24-year-olds has declined in recent years, particularly among malesFewer than one in three adolescents report eating fruit or vegetables daily, while less than half of older girls report eating breakfast dailyThe percentage of children living in absolute poverty rose to 21% in 2006-07 to 2008-09.
Source: 2011 Children and Young People's Wellbeing Monitor for Wales"This may only be the tip of the iceberg as they only cover hospital admissions, so do not include the many young people who do not come to the attention of services."
The assembly government published its action plan to reduce suicide and self-harm in 2008 and Ms Lavis called for current data to show it is working.
Between 1995 and 2008, the number of reported cases of chlamydia among 15 to 24-year-olds in Wales also increased from 192 to 758 per 100,000 population.
Dr Jim Richardson, a former children's nurse with a background in adolescent sexual health research, said this was down to increased awareness.
The University of Glamorgan academic said: "The ways of protecting yourself are more varied and in general people are more knowledgeable about the side and after-effects.
"All the other indicators of sexual health are following positive trends and reflect the hard work which has gone on but more definitely needs to be done."
The study also found the number of babies born with foetal alcohol syndrome in Wales rose by 10% in 2009 - causing concern among experts, despite the numbers involved being small.
Between 2006 and 2009 the number of babies with the syndrome had been falling steadily.
Helen Rogers, head of the Royal College of Midwives in Wales, said more must be done to communicate the risks of drinking alcohol during pregnancy.Continue reading the main story
Local authorities and the new Welsh government post-election must...use this data to develop and review services that will have positive, lasting impact on children and young people's lives”End Quote Keith Towler Children's Commissioner for Wales She said: "This is very worrying and we are always concerned pregnant women who drink aren't taking this as seriously as they should and the real number is under-reported.
"It appears we are not doing enough to communicate the risks - I think this is a symptom of a much wider issue about our attitudes towards alcohol."
Wales already has the highest rates of women who drink and smoke before and during pregnancy in the UK.
Children's Commissioner for Wales Keith Towler welcomed the monitor as a "useful benchmark" and applauded the inclusion of surveys with children.
He said: "Local authorities and the new Welsh government post-election must show they have listened, taken their views seriously and use this data to develop and review services that will have positive, lasting impact on children and young people's lives."
Nearly one in three (32%) of children in Wales now live in poverty.
A consultation on maternity services in Wales ended in April but should see healthy lifestyle options promoted by all health professionals caring for expectant mothers.
In November the assembly government launched a five year plan to reduce teenage pregnancies and STIs.
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