Professor David Southall was struck off by the GMC
Delegates at an annual meeting of paediatricians have voted to express their "grave concerns" at the GMC.
The "disproportionate" ban by the General Medical Council on two paediatricians for their conduct had led to a climate of fear, they said.
Paediatricians are being put off appearing as expert witness in court cases because of a heavy-handed approach by regulators, doctors said.
But the GMC said child doctors rarely face disciplinary action.
Doctors attending the Royal College of Paediatrics and Child Health's (RCPCH ) annual meeting stopped short of backing a motion of no-confidence in the GMC.
Instead they supported an amendment noting their "grave concerns" over current GMC procedures covering child protection complaints.
The paediatricians are calling for more protection for doctors over vexatious complaints and serial complainants.
Dr John Bridson of Professionals Against Child Abuse (PACA) - who tabled the original no-confidence motion - said leading paediatricians who had been disciplined following contentious child-abuse cases had been unfairly treated.
He described Sir Roy Meadow and Professor David Southall, both struck off by the GMC, as "people devoted to the wellbeing of children."
Dr Bridson said: "They did not present a danger to their patients, they were simply doing their job in the way they thought best - and their treatment at the hands of the GMC means many doctors now think twice before reporting their concerns or agreeing to appear as expert witnesses.
"That is not good news for children or their families."
Sir Roy Meadow was struck off by the General Medical Council in 2005 for his "misleading" evidence in the trial of Sally Clark, accused of murdering her two sons.
He had said the probability of two natural unexplained cot deaths in the family was 73 million to one, a figure later widely disputed.
Professor David Southall was struck off after accusing a mother of drugging and murdering her son. The claim was made in an interview with the mother about the safety of her surviving son.
It was the second time in three years Dr Southall had been found guilty of serious professional misconduct, after previously accusing Sally Clark's husband of murdering their children.
But the GMC alleges doctors may themselves be "creating or adding to the very problem they say they wish to resolve".
A spokesman said: "It is extremely rare for a paediatrician to appear before a panel in connection with child protection work. Since 2004, panels have considered more than 600 cases.
GMC PAEDIATRICIAN CASES
May 2005: Camille De San Lazaro is cleared after admitting to overstating accounts of abuse at a nursery
July 2005: Professor Sir Roy Meadow struck off after his "misleading" evidence in the Sally Clark case
Dec 2007: Dr David Southall struck off after accusing a mother in an interview of murdering child
"Only two could reasonably be said to be have been about paediatricians involved in child protection work.
"Our critics are trying to create the impression that the GMC is intent on unfairly persecuting paediatricians involved in child protection work. Nothing could be further from the truth."
The RCPCH had stressed that even if the motion of no-confidence in the GMC had been passed, it would not automatically have become the policy of the College.
"Nevertheless, we are of course aware that the difficulties of working in child protection are a concern for many of our members and we are working with the GMC and other organisations to resolve these issues," said president Dr Patricia Hamilton.