The Premier League also confirmed that 81% of players have had at least one jab.
The numbers mark a large increase in uptake of the vaccine.
“This latest data shows the tide is very clearly turning,” Professor Jonathan Van-Tam, England’s deputy chief medical officer, told BBC Sport.
“It shows that people are listening to sensible messages from well-informed health professionals. That is where you get the good advice from, you don’t get it from the internet, or Instagram or Facebook.
“It is brilliant and is a real positive change.”
Newcastle goalkeeper Darlow urges players to get vaccinated for Covid-19
The Sports Desk podcast: Should sport get tough on vaccine hesitancy?
At the end of September there were only seven clubs in the Premier League where more than 50% of players were fully vaccinated.
“Vaccination rates are collected by the Premier League on a weekly basis and the league continues to work with clubs to encourage vaccination among players and club staff,” the league said.
In an interview with BBC sports editor Dan Roan, Prof Van-Tam believes more players will get vaccinations if not being jabbed compromises their ability to travel outside of the UK to play.
“I think the figures will rise more as it becomes obvious it is going to be difficult to travel internationally without having been vaccinated,” said Prof Van-Tam.
“Football players will undoubtedly want to travel abroad – for leisure time as well as their tournaments and competitions.”
In the English Football League, the BBC understands that, as of September, 49% of players were fully vaccinated – up from 18% the previous month.
Vaccination rates in English football are lower than a number of other sports and leagues, with Professor Van-Tam saying he was frustrated by there not being a higher take-up rate.
“All over the world we have seen, not just in the UK, vaccine acceptance rates for Covid are a bit lower in the younger adult age groups,” he said.
“It is disappointing. Especially when you are someone like me who has given the last 18 months of your life in the quest to get vaccines as quickly as possible for the UK.
“For somebody like me who has burnt a lot of energy and cost my family lots of attention to get there, of course it is disappointing.
“But the latest data we have seen from the Premier League is very encouraging.”