Boston’s dugout was empty early in the afternoon as the Sox threatened not to play their exhibition game against the Jays because of a dispute over payments to support staff for their trip to Japan.

The Providence Journal / Bob Breidenbach

FORT MYERS, Fla. — It started innocently enough.

On Tuesday morning a member of the Oakland A’s staff called Terry Francona and asked if Red Sox coaches were being paid the $40,000 “appearance fee” that the players received for traveling to Japan. Francona assumed they were … but when he looked into it further, he found they weren’t.

That was the beginning of a series of events that culminated in the Sox’ refusing to take the field for yesterday’s nationally televised exhibition game against the Toronto Blue Jays — and threatening not to go to Japan for the week-long visit that includes two regular-season games against the A’s — until the coaches and other support personnel, about 15 people in all, were guaranteed the same $40,000 Francona and the players were getting. The issue was settled about 45 minutes after the scheduled 12:05 p.m. start, the game began at 1:10 p.m., and last evening the Sox boarded a charter for the 17-hour flight to Tokyo that, because they cross the International Date Line along the way, won’t arrive until about midnight tonight Japanese time (11 a.m. Providence time).

“The coaches are a huge part of our success and have been for many years,” said Kevin Youkilis, who is the team’s union representative. “This was just something, as players, that we felt very strongly about. We want to apologize to all the fans at the game who had to sit around a little longer, and to other fans who might have been upset at first, but this is something we felt strongly about.”

Neither the Red Sox nor Major League Baseball will say who came up with the $600,000 to pay the Red Sox staff members. But as they boarded the bus to take them to the airport, Curt Schilling and many other players expressed relief that Red Sox ownership had resolved the problem.

When asked if the team picked up the remainder of the tab, Sox general manager Theo Epstein wouldn’t confirm.

“I don’t think they want us to get into that too much,” he said.

The issue, said Youkilis, stemmed from a breakdown in communication last fall, when the trip was being planned. Ordinarily the coaches are not represented by the players’ union, the Major League Baseball Players Association (MLBPA), unless postseason shares and pensions are involved. But Youkilis said that, after a conference call with MLB and the MLBPA last October, the Red Sox contingent on the call was led to believe that the players, coaches and staff were being handled together.

“I thought we were all under the same [umbrella],” said Youkilis, who added that with so many people on the call it was sometimes difficult to hear exactly who was saying what.

When Francona got the call from Arizona, where the A’s train, he immediately called Youkilis. Youkilis, in turn, checked with the MLBPA. They were surprised — stunned is more like it — to find that the coaches wouldn’t be paid anything extra for making the trip.

“It’s a big deal,” Francona said yesterday morning. “I don’t appreciate that coaches are [viewed as] second-class citizens. That has never sat well with me. We’re over there representing Major League Baseball, and we’ve talked about doing it with class, but this is disheartening. This is hard to understand. We were told [they would be paid] and the players believed it, too. I double-checked on this [over the] winter. This isn’t something I take for granted.”

Overnight efforts to resolve the issue failed, partly because many MLB officials are already in Japan. And when the Sox players arrived at City of Palms Park yesterday morning, they decided to take matters into their own hands.

“From the players’ standpoint, we all felt the same way,” Schilling said. “This can’t happen.”

The Sox held a closed-door meeting and voted unanimously not to play the game against the Blue Jays, and not to board the plane for Japan, unless the coaches and staff were paid.

The coaches — and even the day’s opponent, the Blue Jays — appreciated what the Sox were doing.

“It means a lot,” said hitting coach Dave Magadan. “It’s nice to get some recognition from the players.”

“Anytime there’s this sign of support,” added pitching coach John Farrell, “it’s a reflection of how [the players] view the situation and understand that it’s a combined effort, for whatever task we face — whether it’s preparing for an opponent or something like this. It’s a recognition of the relationships that are built [between players and the staff]. It’s the reason we were able to face so many challenges last year, because there’s a feeling of unity. It’s very much appreciated.”

Many times during the late-morning hours, and during the hour-long delay, Red Sox players, including Mike Lowell and Jonathan Papelbon, discussed the situation with Blue Jays players. Toronto shortstop David Eckstein said his teammates would have understood if the Red Sox hadn’t taken the field.

“They have to do what they have to do,” he said. “They are one [united] team.”

The fans at the park, generally unaware of the drama unfolding before their eyes, were surprised when an announcement came over the PA system that the start of the game would be delayed “because of a dispute between Red Sox players and the Major League Players Association and Major League Baseball.” Predictably, that was met with a chorus of boos.

The Red Sox players stayed in the dugout for about 10 minutes after the scheduled start, then were summoned to the clubhouse for a meeting. They didn’t emerge again for about half-an-hour, but when they did they had their bats and gloves and began stretching. An announcement was made at about 12:50 p.m. that the game would start at 1:10.

The issue had been settled.

“I want to make real clear that this was not a case of players being greedy,” said Francona, who spoke twice to commissioner Bud Selig yesterday. “This was a case of players uniting together, and that’s part of the reason we’re good. There was no disrespect to baseball, and we made sure the Blue Jays knew that. It was a very difficult position we were in and it got resolved.

“I honestly don’t know where the breakdown was and I don’t know if anybody knows right now. I’m sure at some point we’ll get to the bottom of it, but we needed to get through it, move on and play baseball. Our organization stepped up. Our players stepped up and now we can go play baseball.”

When the A’s became aware of the drama unfolding in Florida, they had a meeting of their own in Arizona and also voted not to play their scheduled game and not to fly to Japan. But the resolution arrived about three hours before their scheduled game time. Their coaches will also receive additional compensation for making the trip.

The threat of not to go to Japan could have had larger implications. Under terms of the collective bargaining agreement, the players could not refuse to play a regular-season game. The Sox players were told there would be larger problems if they didn’t play the two games against the A’s.

Still, if the Red Sox proved anything yesterday, it’s clear they are a unified group.

“We have a lot of different personalities and a lot of different players from around the world, but the one thing we have is unity on this team,” said Youkilis. “We stick together and we try to set [aside] our personal differences for the good of the team, and that’s what we did [yesterday].”

Sean McAdam contributed to this report.

jmcdonal@projo.com