Nearly seven in 10 heads believe drinking by pupils of secondary age has increased over the past five years.
In a survey of 119 schools across the UK, the BBC's Six O'clock News found the increase was predominantly noted in the under-16 age group.
A total of 49 heads said drink was a bigger problem than drugs, while 40 said drugs were the bigger issue.
The Prime Minister, Tony Blair, has given a warning that unless more is done to combat binge drinking, the alcohol industry may be forced to pay for dealing with drunken behaviour.
Hangovers
Cheryl Herron, head teacher of Bridgemary Community School in Gosport, Hampshire, said some pupils come into school drunk or with hangovers.
"It sometimes leads to different behaviour that then has a knock-on effect on the rest of the group so their learning is affected."
Ms Herron has seen her school improve from a struggling institution to an improving one in the three years she has been head.
But she is worried about the impact alcohol is having on her pupils.
She was particularly alarmed to find people driving onto the school grounds to sell alcohol to pupils.
"We eventually caught them and they now no longer come on to school site, but they do park elsewhere."
Binge drinking
Sixteen-year-old Sammy, from Leven in Fife, started drinking heavily when she was 13.
She has now learnt to combat her problem, but got into trouble with the police when she was drinking.
"I wasn't really listening to anybody, I just wanted to do my own thing and I just wanted to drink the whole time.
But alcohol abuse counsellors are concerned that unless more is done to turn teenagers away from drinking to excess, too many will find alcohol has shaped their futures.
Joy Patrick, counsellor for the Fife Drug and Alcohol Project, said: "It's a big problem for some young people.
"They don't realise the damage that they're doing to themselves at such a young age, but at that young age, they're 'invincible', you know?"