Jason Leitch has warned the return of fans for next week's Scottish Cup Final is now "at risk".
Hibs and St Johnstone supporters were dealt a blow on Friday after First Minister Nicola Sturgeon announced Glasgow would remain under Level 3 Covid-19 restrictions.
A bump in cases in the area means the city will not join most of the rest of Scotland in Level 2 from Monday.
The SFA's application to allow fans into Hampden for the May 22 showdown - with permission initially granted for 600 punters to attend - was made under the proviso Glasgow was set to have restrictions eased.
But the national clinical now admits the plan is in serious doubt.
"The situation now I'm afraid is that there is no travel in or out of Glasgow," Professor Leitch told BBC Scotland.
"That's just been announced so we haven't had time to talk to the SFA yet. We will of course do that.
"But the rules are no travel in or out for non essential reasons. So that would put at risk, I would've thought, fans coming in and out. And Level 3 stadia can't have anybody in them."
