The pit, which has been run by an employee-owned trust since 2013, closed in June with the loss of 430 jobs.
The Department for Culture, Media and Sport listed the headstocks after a campaign group pushed to save them.
Doncaster Council, which was planning on having the towers demolished, said the site posed a "real danger".
Hatfield was one of the UK's last remaining deep seam mines when it closed after almost a century of production.
After its closure, the Hatfield Main Colliery Community Heritage Association called for the mine head structures to be preserved as a "monument" to the area's history.
Historic England recommended listing the headstocks as they are "the most recognisable feature of the nationally-important coal industry".
The power and winding engine houses at the site were not recommended for protection.
Jo Miller, Doncaster Council's chief executive, said: "We are all immensely proud of Doncaster's coal mining heritage, but the fact is that these dilapidated headstocks are an accident waiting to happen.
"The decision taken by Historic England appears to have been taken with no thought to a funding plan for a decaying structure.
"This will put the public at risk in the short term and could cost Doncaster taxpayers millions over the coming years."
Historic England said it "understood" the council's position and a meeting had been held to discuss "how to make them safe".
At least £1m will need to be spent on the "unsafe" Hatfield Colliery site after its headstocks were given Grade II listed status, a council has warned.