The FIA has granted all F1 teams an extra allowance with which to improve the infrastructure of their factories.
The top teams can spend an extra $6m, the middle-ranking outfits $14m, and the four bottom teams – namely AlphaTauri, Williams, Haas and Sauber/Alfa Romeo – can now invest an extra $20m.
However, Bayer, who helped create the cost cap and the financial regulations when working for the FIA, says that that extra funding is not available to the team.
"I think the first question to ask really is do we have the money?," he told Motorsport.com when asked about the CapEx allowance.
"Because we haven't forecasted any of that money when we went to meet the shareholders for the budget planning. So I have to say that I'm not really a big fan of it, to be honest.
"I was, as you know one of the architects of the cost cap, and we set out to level the playing field. Now, I understand that sometimes we need to make adjustments, and we did.
"But I think it's difficult to understand. Because you make a plan, you sort of focus on where you spend the money. And then a month later, everything's changing and you're like, 'I made my plan. These guys maybe knew something I didn't know.'"
While Williams already had funding earmarked for CapEx investment, and Sauber is keen to ramp up its Hinwil base ahead of Audi's takeover, Bayer says it's not as straightforward for AlphaTauri to find that $20m.
"For us, it's a lot harder, definitely," he said. "And at the same time, if you're looking at the top teams, it might not be fair either. Because I remember when I saw the numbers in the initial cost cap phase, I saw the real budgets of Ferrari and Red Bull and all of them.
"And literally we didn't understand how they will actually squeeze all that money into a cap. And they managed to do it. And now things are changing again. I'm not so happy about the whole situation."
Bayer also referenced the separate wind tunnel allowance which has helped both Aston Martin and McLaren invest in brand new facilities.
"I think the conundrum of it really is now that the door is open, you have to go and spend," he said. "Because the cap is limiting the spend, it's defining the performance.
"Once you open the cap, it's a bit like the wind tunnel. When Lawrence [Stroll] got the wind tunnel, suddenly new wind tunnels were popping up. Despite the fact that before that everybody said the future is CFD! So there you go, we'll spend more money."
Bayer conceded that he knows where AlphaTauri's Faenza facility can be improved if the team can find the money.
"I have a wish list, always," he said. "Probably, top of my head, I would go for a very, very nice simulator."
