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That could change once the surgeon can fully assess the damage during the operation, and Latics are keeping their fingers crossed that his absence won't be lengthened.
Manager Paul Jewell had been bracing himself for bad news since Frandsen was stretchered off in the second-half of Saturday's 4-0 hammering of Sheffield United.
He was hurt after clashing with United's Alan Quinn in a midfield tussle, their knees knocking together before Frandsen twisted sharply.
Jewell said: "Unfortunately the scan has shown Per has damaged ligaments in his knee and he's having an operation today to put it right.
"It's a bitter blow to lose him because he has been in outstanding form and brought something new to the team.
"Having seen the specialist, Per has been told that he will be out of action for at least three months, but that depends on how his rehabilitation goes.
"We'll know more after the operation today, and all we can for now is wish Per the best of luck for his recovery."
Jewell is now pondering over Frandsen's replacement in the centre of midfield for Saturday against Derby at Pride Park.
The transfer market is one avenue he can take, while there are players already in the squad who can step in alongside Jimmy Bullard.
Recent signing Gareth Whalley would be a straight swap although he still needs match practice after five months without first team football.
Another possibility is to bring Alan Mahon back into the side after being forced to watch all the Championship action to date from the substitutes' bench.
He replaced Frandsen on Saturday, taking up a left-wing role with Lee McCulloch moving into the middle to counter United's physical presence.
But former Republic of Ireland international Mahon can play the central role if needed and caught Jewell's eye during his 20-minute run against the Blades in which he set up the fourth goal.
Jewell said: "I thought Mahon was outstanding when he came on, and wasn't too surprised by that as he had been lively in training on Friday.
"He won a few headers out there, set up the fourth goal and was full of energy.
"He's a bubbly character, a great lad to have around the place, and it's a testament to how well we've been playing that he hasn't been able to get into the team.
"Mahon is a different kind of player to Lee McCulloch on the left, and just at the moment we have been choosing to play Gary Teale on the right wing with Lee tucked in on the other."
Until Saturday, Mahon's only first-team involvement was a start in the Carling Cup defeat to Grimsby a month ago.