Defeat on Monday was England’s fourth from four games in Australia, meaning they surrendered the Ashes at the earliest opportunity.
England again dropped catches, as they did in being knocked out of last year’s T20 World Cup at the hands of West Indies.
Following that exit, Hartley said: “About 80% of the England team are fit and athletic enough, but there are girls in that side who are letting the team down when it comes to fitness.”
Coach Jon Lewis responded by saying he did not believe that criticism was fair, adding that “our players are very fit”.
“I’m surprised that people would say that, actually,” he said. “Fitness was absolutely nothing to do with us losing that game.”
“Clearly I have upset them,” Hartley, who was England’s second-highest wicket-taker in their successful 2017 World Cup campaign, said on Monday.
“Jon Lewis has said there isn’t a problem with fitness in his squad. They think I am wrong, which is fine – I’m entitled to my opinions and they are entitled to theirs.
“It is my job to say something that needs to be better and I did. The way I have been treated since I think has been totally unfair.”
The England and Wales Cricket Board was contacted by the BBC but did not wish to give a response.
Hartley wrote on X on Tuesday: “To be clear, there are some members of the England team who have been really disappointing, but by no means all.
“For some, friendships remain unchanged. For others, I’ve been shocked and surprised by their response.”
