Guidance for coroners, the police and the Crown Prosecution Service should be overhauled to stop unnecessary manslaughter investigations against doctors, the defence organisation said.
It also called on the GMC to reconsider how it handles cases involving GNM, highlighting that under the current process doctors have been unfairly suspended in cases that have not ultimately led to a prosecution.
The fact that more than nine in 10 cases currently investigated do not lead to a prosecution reflects 'a significant level of over-investigation of doctors', it warned in its submission to a review launched by health secretary Jeremy Hunt in response to the case of Dr Hadiza Bawa-Garba.
Evidence from the MDU to the review - led by Mr Hunt's clinical adviser Sir Norman Williams - comes just a day after the GMC published its own submission, calling for legal protection for doctors' reflective notes.
The MDU said advice for coroners needed to be clearer to bring a consistent approach to referral of GNM cases to the police and the Crown Prosecution Service. The MDU has also called for the establishment of a specialist police unit to handle GNM cases.
MDU senior solicitor Ian Barker said: 'There should be far fewer investigations and prosecutions of healthcare practitioners for GNM. It should be about identifying and prosecuting only those cases that are the medical equivalent of deliberately driving down the motorway on the wrong side.
'Coroners are currently responsible for passing most cases to the police for investigation and they should get greater support and clearer guidance about the law. There should be a far more robust referral process, to help to achieve greater consistency and clarity and ensure only appropriate cases are investigated.'
Medico-legal experts have advocated a switch from the current legal framework in England to something closer to the rules in Scotland. Mr Barker told the government review: 'In Scotland we are not aware of a case where a doctor has been successfully prosecuted for the similar offence of culpable homicide. We believe the same approach should apply in England and that investigation and prosecution of healthcare practitioners should be reserved for only the worst cases.'
The MDU highlighted the stress that unnecessary investigations place on doctors. GP leaders have previously highlighted concerns that the rate of suicide rises among doctors facing investigation.