The sports council confirmed the move when it announced its first awards under the scheme, which range from Pounds 1,000 to Pounds 1,500 and total almost Pounds 100,000.
But with primary schools coming on board, the grants may not be as high. Stewart Harris, head of the Team Sport Scotland programme, warned: "There will be the same pot of money available and yet we will also have 2,500 primary schools who can apply in addition to the secondary schools."
The Sports Mark scheme was launched in November and so far 91 schools have benefited. "Recognition" awards of Pounds 1,000 were made to schools with well managed sports programmes sustained over a period of time. "Incentive" awards of Pounds 1,500 were given to schools that are striving to enhance their provision or have plans to do so.
There were also eight enhanced recognition awards: Gryffe High, Tain Royal Academy, Elgin High, Belmont Academy, Boclair Academy, Perth Academy, Queen Anne High and Stranraer Academy.
Stuart Forsyth, head of PE at Stranraer Academy, said: "The money is a fantastic help and we are considering putting it into the sports that maybe do not have a lot, like indoor hockey."
Stranraer has a particularly active extracurricular programme and a senior member of staff acts as school sport manager. Activities are on offer after school on Tuesday, Wednesday and Thursday and staff can join in on Friday.
"We have step classes which some of the teachers join and there is also indoor football where the staff can play with the senior pupils and swimming," Mr Forsyth said.
Stranraer runs football, rugby and hockey teams at under-13, under-15, under-16 and under-18 levels and, in addition to inter-house competitions, a day is set aside in the summer term. All 900 pupils take part in eight sports judged by the teaching staff.
Elgin High showed excellent links with the community whereas Boclair Academy in East Dunbartonshire offered nine sports and a record of excellence in athletics.
Mr Harris says: "Generally we felt that the applications were pretty good and the 91 schools who received awards had good schemes in place. But there were still nearly 400 schools which did not apply. What they all had in common was a variety of provision. It was also pleasing to see schools who had appointed someone with responsibility for co-ordinating sport."
He admits that the money is "a drop in the ocean" but says it does recognise the good work being done.
"The important thing was that this was not something that was foisted upon schools. It was a case of the education sector and ourselves working together to devise a scheme," he pointed out.