The 20-year-old joined the Cottagers in 2008 and has now agreed a summer move to Manchester United for an undisclosed fee.
Stones chairman Paul Bowden-Brown told BBC Radio Kent: "I appealed to Fulham owner Mohammed Al-Fayed and their chief executive but without success."
Smalling's move to Man Utd has already triggered a compensation agreement.
"We agreed with Fulham that for every 10 first-team appearances Chris made, Maidstone would receive £10,000," Bowden-Brown added.
"There was no sell-on clause because Chris was a schoolboy while he was with us and could not have played for England Schoolboys had he been on contract.
"I wrote to Al-Fayed and their chief executive, as did many of our supporters, pointing out our circumstances.
"They responded by saying that Chris had been a rough diamond when they signed him and that their manager Roy Hodgson had developed him.
"There will be no further payment of any sort coming to Maidstone."
The cash-strapped Stones have been unable to pay their players since 5 December and have deferred paying any wages until the end of the season.
Maidstone are seeking to establish a ground of their own in the town, they presently lodge with Ashford Town after leaving Sittingbourne last season.
Source: BBC Sport
Source: BBC Sport