The EFL announced last week that they were charging the Owls after the club sold their Hillsborough stadium for £60m to owner Dejphon Chansiri to avoid breaking spending rules in 2017-18.
If found guilty, the Owls – who say they will “vigorously defend” the allegations – could face a points deduction.
But Monk said: “No-one at the club saw that coming.
“Having spoken to everyone at the club, the club as a whole, I think it was the surprise of it.
“The communication has been fantastic over the last year, between the club and the EFL.
“The biggest part of the surprise is the charges that were put forward were things which the EFL would have ratified and agreed to at the beginning.
“That’s where the strangeness of it, the surprise for the club.”
The timing of the EFL charges appears to have caught out Wednesday, after they were released from a soft transfer embargo to buy and sell players in the summer.
But the League – after reviewing a “large number of documents” regarding the sale – claim there is “sufficient evidence to justify issuing charges of misconduct”.
Under the EFL’s profitability and sustainability rules, Championship clubs are allowed to lose £39m over three years.
Without the sale of Hillsborough, the Owls would have exceeded those losses.
The problem seems to centre on the timeline, regarding when the deal was actually completed and which financial period the funds from the deal should be attributed to.
But Monk insists Wednesday are “very confident” they can defend the charges.
He said: “The message from the club to myself is that they are very confident that everything will get resolved, and not be what everyone is trying to make it out to be.
“Everyone at the club was surprised, they didn’t expect (it) after going through a good period of communication, everything seemed to be on track and fine –then out of the blue, that (charge) comes.
“But that’s a club issue. In terms of myself, players and the staff we have here, it doesn’t affect our daily training, it doesn’t affect that we have to go on to the pitch and try and win games.
“We can only control what we can control, that’s my duty as a manager. It’s the duty of the players and staff to focus on our jobs, which is the football. The club will deal with the rest of it as it goes along.
“That’s what everyone wants (a quick resolution). Football clarity is key to everything, but the club feels it has done everything possible that it can.
“The club will work through that with the EFL, communicate with them, and resolve the matter.”
Monk is no stranger to such financial off-field problems.
He was manager at Birmingham City last season, when they were deducted nine points for breaching profitability and sustainability rules.
“It was a different situation (at Birmingham) in terms of what the charges were,” said Monk.
“At that time, I was unaware we were going to be going into an embargo because of FFP (Financial Fair Play). There were different circumstances behind the scenes, in terms of communication, different to what has gone on here.
“You can see clearly the club has communicated (with the EFL) over the past year.
“It’s clear with how the summer went, with players coming in and going out, that can only happen if there is clear communication.”
The manager’s main task now is ensure the off-field issues do not seep onto the pitch, as eighth-placed Wednesday head to Championship leaders West Bromwich Albion tomorrow.
A points penalty – speculation has seen potential punishment range from 12 to 21 points deductions – could see the Owls go from play-off contenders to a relegation battle.
“We have to stick together and fight every hurdle we come across,” stressed Monk.
“We have to show the type of club we are. Everyone at the club can use that as motivation to be successful.
“It is the same mentality we had at Birmingham. We are going to have difficult moments, good moments, ups and downs, and hurdles put in front of you.
“We have to stick together. That’s not just the players and me as the manager, and the staff, it’s the fans. We have to have that collective togetherness, more than ever.
“My experience helps, in terms of Birmingham, and having the experience and knowledge of trying to help a group understand how to focus on what they need to do.
“That’s the reality, it doesn’t directly affect us, in terms of how hard we can train every day, we can play how we want to play, approach matches to win matches.
“That’s what we have to focus on, and what we have already spoke about. I have seen that mentality during the international break, and we are going to need that – along with the whole club and the fans – to help the team.
“We show how together we are, and we come out fighting. That’s the key for this period and the rest of the season.”