The report said levels of young people smoking was "unacceptable"
Almost one in 10 children aged between 11 and 16 are regular smokers, and 10% of those in treatment for alcohol misuse are under the age of 18.
The 2008 Chief Medical Officers report, published on Tuesday, addresses the challenges to public health in NI.
"We still have an unhealthy relationship with alcohol in Northern Ireland," said Dr Michael McBride.
"We must try and educate our children and young people especially about the consequences of binge drinking."
As of 1 March 2007, 3,736 people were in treatment for alcohol misuse.
Approximately £800m is spent in NI every year dealing with excess alcohol consumption across all age groups.
One in four men, and one in five women drink more that the weekly recommended levels.
The report also said the levels of smoking among young people was "unacceptable".
It added: "An unacceptably high number of children are still exposed to smoke at home or in the car by one or more of their parents.
"High smoking prevalence among manual workers is also an area for concern."
The report also revealed that the average age children were offered drunk, not including solvents, was 13.
Speaking at the launch of the report Dr McBride said swine flu has the "potential to be one of the biggest public health threats we have ever faced".
He continued: "It is important that everyone takes on board how we can all take steps to prevent getting it and to stop the virus spreading to others, and my report re-emphasises this important information."
His report also highlighted growing levels of childhood obesity.
To help combat the problem the Department for Health, Social Services and Public Safety has developed Fit Futures - a plan for joining up health, education and sport.