Falkirk chairman Gary Deans has accused Scottish football's authorities of "unfairness, inconsistency, and double standards" following a meeting of all 42 SPFL clubs on Wednesday.
With all football bar the top two tiers suspended on Monday for at least three weeks, Deans says the meeting provided no "clearer understanding" of why the decision was made.
And he echoed League 2 Stenhousemuir's claim that the lower leagues are being punished for mistakes by clubs further up the league pyramid.
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The 20 clubs in the bottom two divisions - including full-time League 1 outfits Falkirk and Partick Thistle - have been told training is not permitted that all players and staff must stay at home.
"Some decisions, such as those to stop us playing and training while allowing other part-time clubs to continue are baffling," said Deans in a letter to fans.
The meeting was told that the shutdown - imposed by the Scottish FA with support from the SPFL - affects 270 clubs below the top two tiers.
Both Falkirk and Stenhousemuir say there was no consultation from the governing bodies before the decision was made public.
"Quite frankly, our staff and supporters deserve greater respect from Scottish football's decision makers, who threaten their livelihoods and our club with decisions which we believe are ill-thought through and poorly communicated," added Deans.
Dumbarton manager Jim Duffy has expressed doubts over whether the season will restart, and Stenhousemuir chairman Iain McMenemy says lower-league clubs are paying for Celtic's controversial Dubai training camp, which resulted in 16 players and staff have to self-isolate.
"We absolutely have been let down," McMenemy told BBC Scotland. "They've given us over as a sacrifice to appease an angry Scottish government because of problems that have happened elsewhere.
"I'm unhappy with the SPFL. They put out a statement saying they fully support the decision to suspend the leagues. They don't have our full support. I'm not happy.
"We were never asked - the first we heard about this was when we got an email of the statement going out to the media."