A junior doctors' leader urged the British Medical Association to exclude children's health services from the upcoming strike but was overruled, according to reports.
Johann Malawana said it would be a "difficult line to defend" a full walkout because it will affect care given to children and babies.
The junior doctors' committee chairman said excluding paediatrics from the strike was the "right thing to do", according to internal emails leaked to the Health Service Journal.
But his plea was rejected by the committee and thousands of junior doctors will stage a full walkout later this month in protest at controversial Government plans to impose new contracts on them.
In an email to the committee dated March 21, Dr Malawana wrote: "Having taken a lot of very private soundings and talked to lots of people I am going to suggest that any full withdrawal of labour excludes emergency paediatric services.
"I hope the committee will support me in this decision. I think from a (communications) perspective and to try and ensure we get the sign up of [doctors] as well as retaining the reasonable ground, it is the right thing to do."
In a second email on the same day he wrote: "The reasoning being that doctors withdrawing care from children would be a difficult line to defend."
He added: "Even (doctors) not in the services covered I think would feel more comfortable being able to talk about and point to this as something that demonstrates our absolute desire not to take (industrial action)."
Professor Neena Modi, president of the Royal College of Paediatrics and Child Health, called for the Government not to impose the contracts.
She said: "We fully support the provision of effective and efficient primary and secondary healthcare seven days a week but deeply regret that this has been conflated with the imposition of a non-negotiated contract upon doctors in training.
"Paediatrics already has an average 12.5% shortfall in trainee numbers, rising to 20% in sub-specialties such as neonatal intensive care.
"The imposition of the new contract has led to eight resignations of trainee paediatricians in the London region alone in the last three months, more than in the previous two years.
"It is becoming increasingly difficult to sustain the provision of safe healthcare services for UK children."
A BMA spokesman said: "As would be expected, junior doctors, of course, considered the full range of options and possible implications before deciding on what course of action to take.
"No junior doctor wants to have to take any action, they would rather be in hospital caring for patients, but they have already done everything else in their power to make their voices heard. By continuing to ignore them, the Government has left them with no alternative.
"The critical message for patients is that anyone who needs emergency care on the days of industrial action will get it, the only difference is that it will be provided by senior doctors rather than junior doctors.
"For the sake of patients as well as doctors, the Government must listen to concerns from all sides calling on it to lift imposition and get back around the negotiating table. It is not too late to remove the threat of imposition and end this dispute through talks."
Health minister Ben Gummer said: "Senior NHS leaders have been clear that removing emergency cover puts patients at risk and now we learn that even Johann Malawana, who is leading the junior doctors' strike, has personally argued that his colleagues should not participate in a full walkout.
"What we are seeing is an organisation in turmoil and regrettably, that turmoil is now impacting directly on patient safety. This is yet more evidence that the BMA should call off this dangerous and damaging strike."