The EFL have today released update guidance on how clubs can try to minimise the disruption caused by Covid.
They say that 25 per cent of players across its three divisions "don't intend to get the vaccine".
It comes amid rising cases that have seen 10 EFL games called off already - with more likely to follow.
A statement from the EFL said: "The latest vaccine data collated for November has shown that 75 per cent of players across the EFL are either fully vaccinated, have had a single jab or intend to be vaccinated.
"Double vaccinated players total 59 per cent, 16 per cent are set to get the jab, while 25 per cent of players currently do not intend to get a vaccine."
Games that have bitten the dust this weekend include Reading's visit of Luton Town - a game that the Royals had planned to use as part of the club's 150th anniversary celebrations - as well as Cardiff's meeting with Derby County.
No new dates have yet been set for the postponed fixtures.
It comes amid rising Covid cases in the country, with the Omicron variant now spreading fast.
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Rooney said: "Unfortunately we have had a few more cases, players and staff.
"From my point of view I will prepare the team with the players I have got as if the game is going ahead and make sure we are ready while we await a decision from the EFL.
"Basically our medical team has been wiped out, and we have had more players get it. From my point of view it is very unlikely the game will go ahead. We are awaiting on confirmation from the EFL."
That confirmation arrived on Thursday afternoon and it depletes the Championship's offering even further after Millwall v Preston and QPR v Swansea City, along with the Reading v Luton game, were called off.
Bristol City boss Nigel Pearson says his club are encouraging people to get their jabs.
He said of the outbreak in football: "I worry for people's health, first and foremost.
"Sport is a part of our community, a very important part of the social aspects, so just if you look at us as an operation, we have an exceptionally high percentage of double vaccinations in the workforce; players and staff alike.
"We'll also be encouraging people to have the booster. Just in terms of how we operate here, we're doing everything we can to make the workplace as safe as possible.
There was good news on the Covid front for at least one Championship boss.
West Brom were missing four players after testing positive last week. Valerien Ismael is now looking forward to welcoming them back for Friday's trip to his old club Barnsley.
He said: “I’ve been told from the medical staff all the players who tested positive can come back and train. We will go from there. The situation is certainly better than last week.”
The EFL have issued updated guidance to all 72 clubs amid the rising number of cases in football.
They have confirmed clubs will be required to implement enhanced 'red' protocols for first team training settings.
All clubs will be required to carry out daily lateral flow tests from now on.