The Jambos boss was left furious by the official’s display during his side’s 2-1 defeat to Rangers earlier this month.
He hit out at the whistler’s “abysmal” performance and claimed Madden had been Gers’ “12th man” as they claimed victory at Tynecastle.
The former Scotland coach insisted he was free to make his comments after echoing similar views voiced by his Hibernian counterpart Neil Lennon after his side’s Celtic Park defeat back in October.
But the Scottish Football Association compliance officer Clare Whyte has taken a different stance and has now issued Levein with a disciplinary charge under the governing body’s rule 72.
It states that no team official shall “publicity criticise the decision and/or performance of any or all match officials in such a way as to indicate bias or incompetence”.
Levein was left furious when Light Blues frontman Alfredo Morelos netted the winner from an offside position before being allowed to escape punishment despite getting himself embroiled in a feisty running battle with home skipper Christophe Berra.
In an astonishing rant, he said: “I read a quote from Neil Lennon a few weeks ago when they went to Celtic Park and he said that ‘we were playing against 12 men’. That’s how I feel today.
“How Morelos stays on the park and gets through that without a booking I’ll never know. Some of the decisions today were abysmal.
“Austin (MacPhee) phoned (SFA head of referees) John Fleming a while ago after we had three goals against us that were offside because the linesman made mistakes.
“John Fleming suggested that we held the line on the 18-yard line to make it easier for his officials. So we did that today and they still f*****g got it wrong!
“Actually, it’s 13 we are playing against. And the good thing is that Neil Lennon didn’t get any punishment - that’s good to know. It’s really good news that there won’t be any punishment.”
Asked if he had sought out an explanation from Madden after the game, Levein added: “What’s the point, unless he’s got a time machine and go back to fix his mistakes?
“Morelos had loads of fouls where he doesn’t even watch the ball. He just jumps into the centre-backs. There was one where he has smashed Christophe and Bobby said to one of our players: ‘It’s alright, that’s just Morelos - he’s a bit silly sometimes’. Well maybe I’ll tell our players to be silly because you don’t get booked for it! It was an abysmal performance.”
Levein will now have to answer for those comments when he appears before a disciplinary hearing a week on Thursday.