Leeds boss Marcelo Bielsa led criticism of the regionalised return of fans as part of the government's new strategy for tackling the coronavirus pandemic.
Bielsa believes the move to allow clubs in tiers one and two to let in a limited number of supporters will "penalise" clubs in the highest tier who must continue behind closed doors.
Bielsa's fears were given qualified backing by Brighton boss Graham Potter, while Bolton boss Ian Evatt described the regional system as "madness" and "crazy".
Bielsa said: "It shouldn't be about the category, or the consequences of being in a category, it should be about trying to maintain the competition as equal as possible with things that are controllable.
"The presence of fans has an effect on the results.
"What the organisation says is people who are from places where there's a higher risk of infection, it means they will be penalised."
Arsenal will be the first Premier League club to welcome fans for a competitive fixture since March after confirming 2,000 spectators will be allowed in for their Europa League match against Rapid Vienna next Thursday.
West Ham's match against Manchester United on December 5 is set to be the first Premier League game with fans in attendance.
Potter, whose side host Southampton on December 7, also expressed misgivings but warned it would not necessarily work in the favour of the home clubs in question.
"Sometimes the home crowd is with you, because you are playing well, and sometimes the home crowd can be a little bit nervous or frustrated and therefore it can work against you," said Potter.
"But I think certainly if you have got that environment, where the home supporters are really behind the players, there's a real belief, a real connection, then I think it can be really powerful at a football club."
Evatt, whose club, like Leeds, are in tier three, was more outspoken, adding to the Bolton News: "I think there is an advantage there – certainly having supporters that are trying to back your team and will them on, it can only help (them)."
In respective statements, Arsenal described the imminent return of fans as an "historic moment for the club", whilst the Hammers cautioned that a "small number" of fans could be allowed to return.
All the games preceding the Hammers' clash with United – Aston Villa v Newcastle on December 4, Burnley v Everton and Manchester City v Fulham on December 5 – are being played in tier three areas.
Brighton, Chelsea, Tottenham and Liverpool are the other teams in tier two areas hosting games that weekend.
In the EFL, Cambridge and Northampton were among the first clubs to announce they were working on piloting the return of fans in matches in the first week of December.
The Rugby Football Union has announced it will allow 2,000 spectators into Twickenham for England's final Autumn Nations Cup match on December 6.
Worcester are the first Gallagher Premiership team to welcome fans after the November lockdown, when Bath visit Sixways on December 5. The Warriors have confirmed a crowd of 2,000 will be able to attend the match.
The PA news agency understands World Snooker Tour officials are exploring the possibility of allowing some fans to watch next week's final stages of the UK Championship in Milton Keynes.
Racegoers could return to courses as early as Wednesday, with Ludlow, Lingfield, Haydock and Kempton all in tier two areas.
