Gale, Yorkshire's new head coach, accepted the absence of Joe Root due to his heavy workload in international cricket. But Bairstow, who has hardly played since the conclusion of England's Test tour to India in mid-December, has also been rested despite having been made available for the IPL.
When Bairstow was not picked-up in the IPL auction, Yorkshire might have presumed he would be available for them. But, despite having played just three days of cricket this year (a warm-up game and an ODI in India, and a warm-up game in St Kitts), Bairstow has instead been rested from the opening two matches of the Championship season, appearing instead as an analyst on Sky's IPL coverage.
That has left Yorkshire, who wrapped up a crushing win over Warwickshire at Edgbaston on Monday after losing their opening game, confused and disappointed.
"I can see why someone like Rooty would want a rest given the amount of cricket he's played," Gale said. "But Jonny has played one one-day international since Christmas. I think he's played three days of cricket.
"For me, he should have been available right from the first game of the season. He had enough time off from the end of the West Indies trip. I felt he should have been available."
It's not the first time that Yorkshire, and Gale in particular, have expressed their discontent with decisions made by the England management. At the end of last season, with the Championship title at stake, Gale was frustrated by Adil Rashid's decision to miss the final match of the season (Rashid claimed that a family member was ill), while the club also requested the release of players from the England touring squad in the Caribbean at the start of the 2015 season. That squad contained several Yorkshire players who were deemed surplus to requirements from the Test side.
Both Root and Bairstow will be available for Yorkshire's next Championship game which starts on Friday. Liam Plunkett, who has a calf strain, is not thought likely to be fit to return.
Gale's concerns have been eased somewhat by the emergence of Ben Coad, who had played just one Championship match before this season, but is currently the leading wicket-taker in the country with 18 from the first two matches, including his maiden five- and ten-wicket hauls.
Only winning a place in the side due to the absence of several first-choice bowlers (Plunkett, Jack Brooks, Ryan Sidebottom and, for the opening match, David Willey and Rashid), he has again demonstrated the depth of the Yorkshire squad and the success of their youth development.
"When you have fine seamers injured you are a little worried," Gale agreed. "But it creates opportunities and Coady has grabbed the bull by the horns and put his name in the hat for the rest of the year. I'm sure the lads will looking over their shoulders thinking how they will get back in the team.
"He's surprised himself. He's always had the talent and done well in the second team but to come in and take 18 wickets, I didn't expect him to lead the attack.
"We pride ourselves on bringing through homegrown players with the time and money we put into the academy. We don't want to be signing guys from around the country or abroad. We want to back our home-grown players. We will always give them the chance first and then the academy lads can see a path into the first team and that gives them hope.
"This is part and parcel of being part of Yorkshire. We've always wanted to bring our homegrown players through, but if we do that, they are going to get picked for England. We want our players to play for England, but when they're available we want them to play for us as well."