By 2014, SNP ministers want every primary pupil to receive at least two hours per week of physical education, while secondary schools are expected to provide two periods of PE per week – some 100 minutes.
Data from the Scottish Government's Healthy Living survey show 84% of primary schools met the target in 2012 – up from just 3% in 2004/05.
More than 90% of secondary schools are now providing two periods of PE, compared with 46% in 2004/05.
Four local authorities met the targets in all of their schools – East Ayrshire, East Renfrewshire, South Ayrshire and West Dunbartonshire – while Glasgow succeeded in 99% of its schools.
Shona Robison, the sport minister, said the upturn would provide a boost to pupils' health, educational attainment and life chances.
"PE in school is a crucial long- term investment, as habits formed in childhood and adolescence continue throughout adulthood, and pupils who take part in PE can better understand the benefits of a healthy, active lifestyle," she said.
"While we still have some way to go, these statistics demonstrate good progress and we are investing nearly £6 million over the next two years to support local authorities with this."
Stewart Harris, chief executive of national sporting body sportscotland, described the figures as encouraging.
"An important component of the world-class sporting infrastructure we are developing in Scotland is the provision of excellent facilities alongside quality teaching and coaching for young people of all ages and abilities," he said.
"In doing so, we are providing the opportunities for Scotland's primary and secondary pupils to adopt healthy lifestyles that they continue into adulthood."
However, Liam McArthur, education spokesman for the Scottish Liberal Democrats, attacked the Government for failing to meet the targets it set itself in 2007.
"It's odd that ministers have found these figures a cause for celebration as they highlight the fact the SNP still hasn't delivered its 2007 manifesto pledge," he said.
Other figures released yesterday by the Government show the take-up of schools meals is continuing to improve after a worrying drop-off after healthier menus were introduced.
Successive Scottish Governments have tried to improve the quality of school meals, but thousands of pupils voted with their feet by switching to packed lunches or eating from take-aways instead.
In 2007, 45% of secondary pupils took school meals, but by 2009 the figure had dropped to 39%. The latest figures show nearly 42% of secondary pupils are now taking school meals.
Other figures highlight the educational inequalities that continue to be faced by children who are in care.
The percentage of looked-after children who left school during 2010/11 and went on to further study, training or who got a job was just 55%, compared with 87% of all school-leavers.