The peer, one of Britain's foremost film producers, is chairman of Unicef UK and Futurelab, an education innovation think tank.
The education system seemed "out of sync" with all that counted for young people, he said in a speech to education ministers from around the world at the Moving Young Minds conference in London this week.
"We are seeing growing levels of both physical and what I can only describe as 'emotional truancy'."
Children were disengaging from formal education, he said, because it did not reflect their experience of digital interaction. And computer-literate young teachers were leaving the profession to enjoy "golden careers in the private sector", he said.
He feared that schools would be relegated to a low status. "We could find ourselves with an education system that is felt to be ever-more irrelevant to the very learners it should be serving," he said.
Lord Puttnam's words came as the Government warned against unsupervised computer use.
Jim Knight, the schools minister, announced an extra pound;30 million to help low-income families buy computers - on top of a pound;60 million fund targeted at 1,000 schools in deprived areas. Ministers also want parents to have access to school databases, so they can check on their children's progress.
But Mr Knight told parents they should protect children from harmful material by not allowing them to have computers in their rooms. Speaking at the Bett education technology conference in London this week, he said that computers should always be in communal areas.
The TES revealed last year that progress had stalled in getting children online at home: about one million children still do not have access to a computer at home.
Becta, the education technology agency, is working with 50 schools and four computer firms to find ways of providing families with cheap computers and broadband.
A large assessment company is also trying to get parents involved by giving teachers and parents online reading lists targeted to children's abilities and interests, not just their reading age.
GL Assessments, which provides tests and assessments for 85 per cent of schools, launched the new internet tool this week.
Graham Taylor, the company's head of online assessment, said the US-style measures would help personalise children's learning.
The assessments would allow teachers and parents to identify appropriate books by authors such as JK Rowling or Jacqueline Wilson.
A YouGov survey commissioned by RM, one of the technology companies working with Becta, found that almost all children did some homework on a computer, and 77 per cent used the internet daily.
Three out of five used social networking sites such as Bebo, and even more played video games, used mobiles or digital cameras.
Young people believed that understanding technology was almost as important in life as having a good teacher or a supportive family.