New figures show 96 per cent of all schools are delivering two hours of PE each week, with 98 per cent expecting to be on target by August. The figure has risen from 89 per cent last year and just 10 per cent in 2004/05.
However, though primary schools saw a big jump in those meeting the targets- from 88 per cent in 2013 to 97 per cent - the number of secondary schools achieving the standard dropped from 91 per cent to 90 per cent.
Scottish Green Party MSP Alison Johnstone said the fall in secondary schools was a "real worry". She said: "It suggests the Government has taken its eye off the ball. We need proper facilities and proper coaching so that exercise remains attractive and enjoyable as our young people progress through the school system."
However, the figures were welcomed by Cabinet Secretary for Sport Shona Robison, who described them as an example of the "excellent progress" being made.
The figures were published as council umbrella body Cosla and Ms Robison jointly unveiled a £6 million new sport strategy for children - called Giving Children and Young People a Sporting Chance. The two-year strategy aims to make Scotland a better environment for young people to embark on lifelong participation in sport.
Ms Robison said: "Scotland is striving to become a healthier, more active nation and we will continue to work to build on this performance."
Cosla spokesman Harry McGuigan added: "We want our young people to participate in and enjoy sport, but we need to create the right opportunities."