Despite the country emerging from the worst of the recession, the Health Behaviours in School Children survey reveals more children are going to school or bed hungry.
It found 22% of children suffered as there was not enough food at home compared to 21% in 2010.
“Similar to our last survey, there are still worrying levels of children going to bed hungry and skipping breakfast,” said Mr Varadkar.
According to Barnardos, two children in every classroom are living without basic necessities through no fault of their own, or their parents.
“They are going without warm winter clothing, living in sub-standard housing and even going hungry,” said Barnardos chief executive Fergus Finlay.
Barnardos policy development officer Niamh Kelly said a child going hungry was a clear sign they were experiencing deprivation.
“A hungry child will not be able to concentrate well in the classroom and may experience poor health as a knock-on effect,” she said.
The study, conducted in collaboration with the World Health Organisation regional office for Europe also raises concerns about levels of cyberbullying.
The survey of 13,611 children in 230 primary and post-primary schools found more girls (17%) than boys (10%) suffer cyberbullying.
Fewer younger children report being cyberbullied and there are, statistically, no significant social class differences.
The number of children engaging in physical fights in a previous 12-month period has fallen from 34% to 29%. Bullying has also fallen from 16% to 13%. Overall, 25% of children said they had been bullied in school once or more in the past couple of months, a 1% increase since 2010.
More teenagers are having sex: The percentage of 15 to 17-year-olds reporting they had sex had increased from 23% in 2010 to 27% in 2014. Of those who had sex, one third (33%) used a contraceptive pill and 73% said they had used condoms.
The number who smoked tobacco fell from 28% in 2010 to 16%. Fewer than one in 10 (8%) smoked, a decrease from 12% in 2010.
The survey also found that the number of children who had never had an alcoholic drink had increased from 52% in 2010 to 58%. One in five (21%) said they had been drunk, a decrease from 2010 when almost one third (31%) said they had been intoxicated.
Asked about drug use, 8% said they had used cannabis in the last 12 months, a decrease from 9% in 2010.
The Irish Cancer Society said the dramatic fall in young people smoking showed Ireland could become tobacco free by 2025.
“Children are now being turned off smoking,” said the society’s head of advocacy Kathleen O’Meara.
“This continuing downward trend is the result of hard work on the part of the Government and health services to discourage children and teenagers to take up something that kills 5,200 adults every year in Ireland.”