The Medical Protection Society (MPS) want parliament to halt plans to introduce a lower standard of proof at fitness to practise hearings.
The proposed Health and Social Care Bill will require the General Medical Council (GMC) and other professional regulators to use a civil standard of proof when disciplining professionals.
Stephanie Brown, director of policy and communications at the MPS, said: "There is a very real risk that reducing the standard of proof will further undermine the confidence of doctors at a time when there are sweeping changes to healthcare delivery requiring the full engagement of the profession."
Under the new bill, healthcare organisations would also be obliged to appoint a "responsible officer to oversee the conduct and performance of doctors.
But Stephanie Brown says that the MPS has "serious concerns" about this proposals to make every doctor accountable to a "responsible officer".
She adds: "We have seen a real variation in the quality and fairness of existing local disciplinary procedures.
"Doctors under local investigation frequently feel that there is a background agenda of interpersonal disputes, politics and power struggles.
"It is essential that the new regulatory procedures are underpinned by fairness, accountability and consistency in order to command the confidence of the both the public and the profession."