Mitchell Marsh was ruled out of Saturday's game at Ahmedabad and could potentially miss other matches after heading back home to Perth for personal reasons.
Fellow all-rounder Glenn Maxwell is also unavailable after suffering concussion following a golf accident this week.
"Yeah, it's not ideal. Both have been star players of the tournament so far at different times," Cummins, whose side are third in the table with eight points and looking to shore up a semi-final spot, told reporters.
"That's the way it is. We knew at the start of the tournament we were going to need a full squad of 15.
"And yeah, I'm not even sure we've played the same 11 two games in a row through injury or selection. So, it's kind of unfortunate, but we knew over a two-month tournament you're going to have to chop and change a bit."
Cummins said Maxwell, who has been in superb form in the tournament and hit a 40-ball hundred against the Netherlands, could return for their game against Afghanistan next week.
"He's trained well yesterday and still taking it day by day, but hoping he'll just miss this one game and then Mitch, we'll wait and see," Cummins added.
"He'll definitely come back. I don't think it'll be a super long trip back home to Perth, but the main thing is he's back home and we'll give him as much time and space as he needs."
Cummins, whose side will finish their pool campaign against Bangladesh, hoped there would be no more issues with unavailable players heading into the knockout stages.
"We need to obviously make the semis, but hopefully this is the last little hiccup where we've got a smaller squad to pick from and then once we get closer, we've got a full squad," Cummins added.
"But I've got in my mind on the main 11, the way we want to play. Really happy with our squad. We've shown throughout this tournament we've been able to mix up the batting order and anyone that's come in has stepped up and done well."
