The Football Medicine and Performance Association (FMPA), which represents doctors, physiotherapists and sports therapists working in the game, said a survey of its members found a significant number do not feel they fully understand their "role, responsibilities and potential liability" in relation to the return to training.
An FMPA statement said that "almost 50 per cent" of respondents within the Premier League raised concerns, with that number rising to 68 per cent in the Football League.
FMPA chief executive Eamonn Salmon said: "It is clear that members do not feel they have been effectively communicated with.
"It is also unfortunate that the FMPA was not asked to consult its members alongside the League Managers Association and Professional Footballers Association throughout this process.
"I believe this sent the wrong message to our members and implied, unwittingly or not, that their views were not required. As frontline staff who are implementing these strategies, their collective views should have been heard."
Salmon said the FMPA was yet to receive a copy of the medical protocol from either the Premier League or the EFL.
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