Little, whose association represents 55,000 youth players and 14,000 adult volunteers, admitted it was unlikely that money owed prior to this season would be recovered. However, the SYFA is now pursuing 147 payments of £10 due from the start of this season - none of which has been honoured.
If this season's trend was reflected since the training fund contribution was introduced by the Scottish FA in 2006-07, well over 1000 payments due to boys clubs via the SYFA have not been made - meaning at least £10,000 has been lost to the grass-roots game.
While the onus has been on the senior clubs to pay, Little said it had been almost impossible to police until this season. "The difficulty we had was the registrations were paper-based," he said. "There just wasn't a mechanism to ensure payment.
"Over the period since 2006 we have received the sum of £20. That's just two payments and both were at my behest after information fortuitously came to light. We have taken the huge leap forward in that we have an online registration system."
Asked if £10 is adequate compensation, Little said: "It should be higher. If it wasn't for the work of our 14,000 volunteers, transfers higher up the food chain wouldn't happen.
"What's required is to sit round the table with all parties in the game and come up with a sensible figure."
The issue of the non-payments came to light when Musselburgh Windsor FC wrote to Scottish FA compliance officer Vincent Lunny to complain about Hearts and Rangers not having compensated them for two outfield players and a goalkeeper. It emerged last night that the East Lothian club has withdrawn the complaint against Rangers after new information which has come to light.