The National League system below steps 1 and 2 have been cancelled, meaning there will be no promotion or relegation of clubs between steps 3 to 6, as well as no promotion to step 2.
But Neville, whose club Salford City rose from the Northern Premier League to League Two, believes it was the wrong decision.
Writing on Twitter, the former Manchester United defender said: "Can someone explain to me what is forcing the non-league divisions to void the season?
"We've been down there with Salford for five years so we have some experience of it and I don't get it!! Help'."
The FA statement read: "Today's steps take into account the financial impact during this uncertain period, whilst considering the fairest method on how the sporting outcomes for the season will be decided with the integrity of the leagues in mind.
"The FA and NLS steps three to six have reached a consensus that their 2019-20 season will now be brought to an end, and all results will be expunged. This will mean no promotion or relegation of clubs between NLS steps three to six, and no promotion to NLS step two."