UPDATE: Queensland Reds trio Izack Rodda, Isaac Lucas and Harry Hockings have all been stood down after refusing to agree to salary reductions.
The Reds returned training on Monday but those three players were notable absentees after deciding not to agree to pay cuts as the sport deals with the coronavirus pandemic.
Under the RUPA - Rugby Australia pay deal signed last month, players were set to take an average salary cut of 60 per cent until September 1, while some of Australia's highest-earning players were offered the option of an overseas sabbatical to recoup their financial losses.
The potential dispute was first raised roughly 10 days ago but the issue was brought to a head on Monday on the first day of training after the Reds made the decision to stand the players down.
Johnson revealed on Monday that Rodda was among the group of six players who had been offered an overseas sabbatical but is still refusing the pay deal.
Rodda, Hockings and Lucas are the only players who have objected to signing up to the modified pay agreement out of Australia's 192 professional players.
Rodda and Lucas are both signed on long-term deals with Queensland and Australian rugby while Hockings comes off contract at the end of the 2020 season.
"For mine, if we're talking about disappointment they're three guys of national interest," Johnson said.
"Two of them we signed long contracts for and the third we were in the process of, he had an offer on the table for an extensive period. It's disappointing because they're front of mind when it comes to the bigger picture.
"We have a high respect for them as rugby players, we think they are part of the solution of the future going forward.
"We showed commitment from our end because we value their talent.
"So that's where the disappointment lies to me because we had a good plan going in place at the moment with youthful people that were committed.
"They've got a few things to work out themselves and then hopefully it gets resolved from a positive light."
All three have the same manager, Anthony Picone but QRU CEO David Hanham refused to be drawn on the influence of their agent in that decision, saying only that it was ultimately the players' call to sign up to the amended pay deal.
Picone said he would make a statement about the situation at an appropriate time.
Players were briefed on the decision on Monday and Hanham said he had spoken personally with captain Liam Wright about the situation.
"I've only spoken to the captain, I haven't spoken to the whole team, they're getting briefed today," he said.
"They're mates. I spoke to Liam, he's disappointed as you would be if you've worked with these and played with these guys since you're a kid, so but at the end of the day they know it's something we're dealing with and i just want them focused on getting ready for a competition to play their best footy and win."
Hanham expressed his disappointment in the situation but would not be drawn when asked if he viewed the players' decision as selfish, given Australia's professional players have all been asked to make the same financial sacrifice.
"I think you come back to our values," he said.
"With the team it's about mateship, it's about accountability, it's about resilience, it's about care for the cause.
"We've all got a care here to see the Reds be a successful football program and we've been working hard on that and also we represent the game of rugby in the state.
"When you put your heart and soul into it, clearly people that are a part of that, feel like they want to be on that journey and others obviously make a decision not to."
Aside from the player deal, the QRU has undertaken widespread cost-cutting measures across the business with the vast majority of administration staff working reduced hours commensurate with the JobKeeper provisions.
With Rugby Australia targeting a competition return on July 4, another player pay deal will be renegotiated once a draw for that competition and a broadcast deal are finalised.
At Rugby Australia, three-quarters of staff, both high performance and administration, have been stood down while the remainder below the executive level are working on vastly reduced hours and pay.
The executive has taken a 30 per cent pay cut.
With the financial future of the game uncertain, former CEO Raelene Castle had publicly projected reduced player contracts down the track, though she was confident that all current deals would be able to be honoured.
Japanese contracts, particularly, are shaping as lucrative options for players around the globe with Top League salaries so far unaffected by the pandemic.
The news comes after a handful of South African players took up options to walk away from their contracts under the SA Rugby pay deal.
Lions hooker Malcolm Marx and Stormers forward Pieter-Steph du Toit have both exercised that option, which South African players were given until May 21, to avoid major pay cuts.