Both were given 12-point penalties at the end of last season but Bury have not even been able to start the new campaign, while Bolton cancelled Tuesday's game against Doncaster due to welfare concerns about their young players that had been forced into action.
The Shakers now face the very real prospect of being ejected from the league come midnight tonight if their owner Steve Dale cannot prove he can fund the club.
"It's becoming farcical,” said Holt.
“I know they like to talk about the 18 million fans every season but it's very difficult to argue the league isn't in trouble when you look at Bury and Bolton, and they're not the only two on the edge.
"This situation has been allowed to develop. We have known clubs were getting deeper in debt for years. Combined debt in the Championship is £1 billion.
"I like Debbie Jevans, I think she has a lot of integrity, but the problem is as clear as the nose on your face and it can't go on like this."
Stanley’s first scheduled home game of the season was cancelled because of Bury's difficulties but Holt's frustration goes far beyond that, as he runs his club on a tight but sustainable budget, in compliance with the league's rules.
"The real problem isn't owners like Steve Dale; it's the system. It encourages clubs to stretch themselves,” he said.
"I want to make Accrington a decent club that will be around forever but, the way things are, the logical thing is to gamble.
"It's not a coincidence that all these owners in the EFL have all gone bad at the same time - it's the system."
Holt said he did not blame the likes of Derby owner Mel Morris looking for loopholes in the rules, such as selling a club's stadium to a related party and leasing it back, because "what choice did he have when you have the vortex of the Premier League sucking all the money in the game upwards?"
As Holt mentioned, Bolton and Bury are not the only two clubs to have experienced financial difficulties in the last 12 months, with Macclesfield, Morecambe, Notts County, Oldham, Oxford, Reading and Southend all failing to pay wages on time at some point last term.
Asked for a solution to the crisis, Holt said: "One simple change would be to immediately treat the non-payment of wages as an insolvency event, which it is, by the way.
"That should be a three-point penalty but it should also ring a huge alarm bell for the EFL to go in and help the club. They should send in a football administrator.
"It's criminal to let these 130-year-old clubs go bust. It's a football problem and it's on us to sort it out. But if you sit back and do nothing, you're complicit."