By the time the SPFL Premiership split arrives, the Inverness Caledonian Thistle manager will have prepared his squad for 16 games in nine weeks.
In the event of serious injury, where a lack of recovery time appears to be a contributory factor, Hughes feels the bodies who devise and revise the fixture lists could be exposed to court action.
Inverness, who reached the League Cup final and William Hill Scottish Cup last eight, have been spared matches in just one of the last seven mid-week slots and have tasted victory in just one of their last eight outings.
Hughes, preparing for a "must-win" home game against Motherwell tonight, said: "We are coming through a really hard programme but we need to keep digging in there. We need to keep going. It was two points dropped at the weekend but we move on to Tuesday against Motherwell. Our programme has probably been the heaviest of any team in the Premiership.
"Myself and Jackie McNamara [Dundee United manager] were just talking about Scottish football the other day. One of the things we chatted about was that we are getting to the point where you'll get somebody actually suing the SFA. You know why? They'll go out there and pick up an injury and say to the SFA 'it's your fault because of the programme you've put in place'.
"They will say 'I'm still playing football in what should be recovery time. In my recovery time, you're making us play games.'
"Ask the sports science people what you need for recovery. The SFA should work with that and make sure they spread their games out a little bit more. I'm only raising that because we've been hit with a really heavy programme."
The Highlanders have sustained realistic European aspirations throughout most the season, but now sit 10 points behind Aberdeen and eight behind Stuart McCall's side.
Hughes was under no illusions as to how important three points were tonight. "We have to go and win it if we have aspirations of going and getting that European spot," he said. "We're still battering on, cracking the whip. The last time we played Motherwell they beat us by two goals. It was a good game, but we really need to try to pick up the three points."
Hughes also voiced concern over how the deteriorating condition of the Caledonian Stadium playing surface is affecting his team.
Again, alluding to the SFA, Hughes criticised the diktat that links funding with playing under 20s matches at your home stadium.
Hughes said: "We're trying to play a certain style of football, but the pitch condition here isn't great. To get your finance from the SFA, you have to play your under 20s games on your main pitch - and it is damaging our main pitch. It is something we are going to have to look at, but it's finance.
"If you're looking at the brand of football we want in Scottish football - get the ball down and pass it - we need to sort that. It's not the groundsman's fault. We're all in it together. We could do with moving our under 20s somewhere else, but then we lose our finance.
"Want to know something else? I'm coming up for 50 and I love saying it how it is. In Scottish football, some of the administrators' decisions are absolutely bizarre."
Hughes, meanwhile, praised the contribution of teenagers Liam Polworth and Ryan Christie who have impressed lately, both performing well in Saturday's 2-2 draw with St Mirren.
Christie, who earned his first start in the match, is the son of club great Charlie, while Liam's dad Iain also served the club with distinction.
"I don't have to place faith in Ryan and Liam. They're there on merit," added Hughes before arguing for their inclusion in the national set-up.
"The way they train is absolutely different class. It's great they are local boys. Polworth coming in needs to believe in himself and needs to show that bit of gallus. His football talent is absolutely different class.
"Liam should be in Scotland under 21s and young Ryan should be in Scotland under 19s. Is it going to be decided on merit or are you only going to play for Scotland under 19s if you are elite academy?
"Is it Mark Wotte [SFA performance director]? All of a sudden we produce one of our own and it goes against the grain. Get Ryan in the Scotland under 19s. Technically, he is as good anything I've seen."
As for the visit of Motherwell tonight, Hughes reported no fresh injury concerns, but doubts remain over captain Richie Foran and winger Aaron Doran.