With the country's Covid-19 rules set to change on Monday, May 17, five days before the final, up to 500 fans can attend under level two regulations.
In addition, clubs can apply for a higher capacity, according to national clinical director Jason Leitch.
Hampden Park is hosting matches at the European Championship with 12,500 supporters scheduled to attend.
By the time of the final the stadium is said to be in the hands of Uefa as they prepare for the tournament.
Supporters group We Are Perth have called on talks to talk place urgently about getting fans into Hampden Park or moving the final to a stadium where they would be able to attend.
Jamie Beatson, editor of the St Johnstone fan site, said: "We are in the absurd situation where there will be fans allowed to attend the SPFL lower league playoff finals - but not the biggest single game in the Scottish season.
"Those games are the same weekend - but there seems to be no will from the SFA to even attempt to get fans, who are the lifeblood of the game, into the match.
"If it can't be at Hampden, find another stadium - any stadium - that can host it, and set a capacity accordingly.
"There is still time, but only if they move now.
"From a Saints perspective this could be the biggest game and - if we are lucky enough to win - the biggest achievement in our club's history.
"Hibernian fans will no doubt feel the same - this could be the best season in their recent history if they sealed third place and the Scottish Cup in the same year.
"It is huge for both sets of fans, who have been locked out of stadiums for over a year now.
"There has been a good reason for that - but the rules are now being relaxed and it will be galling for us to watch fans in stadia north and south of the border over the next few weeks, only for us to be locked out of such a massive occasion."