Health officials have been cautioned by leading human rights experts to ensure that the new contract for junior physicians does not "unlawfully indirectly discriminate against some doctors".
The Equality and Human Rights Commission issued the warning after the Government's own equality analysis states that there are "features of the new contract that impact disproportionately on women".
The analysis of the controversial new contract for junior doctors in England, which was published last week, states the contract may "disadvantage" women working part time and single parents. There may also be "adverse impacts regarding maternity (leave)", it states.
But the assessment concludes: "While there are features of the new contract that impact disproportionately on women, of which some we expect to be advantageous and others disadvantageous, we do not consider that this would amount to indirect discrimination as the impacts can be comfortably justified."
Responding to the analysis, the Equality and Human Rights Commission said: "It is important that Government ensures the new contract of employment for junior doctors does not unlawfully indirectly discriminate against some doctors, and that it properly considers the potential impacts of the contract on equality of opportunity.
"This should include considering the effect of changes to the rules on career progression and pay protection of doctors who take maternal, parental and other leave."
The comment comes as it was revealed that Health Secretary Jeremy Hunt is facing a second legal challenge to try to block the imposition of the contract.
The NHS staff campaign group Just Health is arguing that Mr Hunt has no legal right to force the new contract on junior doctors, and that he has not properly consulted all relevant parties.
The group has issued a letter before action - usually the first step in taking disputes to court - to Mr Hunt.
Campaigners took the move after raising £100,000 over four days through a crowdfunding website to bankroll the proceedings.
It heaps further pressure on Mr Hunt, who facing a legal challenge from the British Medical Association (BMA) over the contracts.
The BMA is arguing the Government has failed to "pay due regard" to the equalities impact of the new contracts.
Meanwhile, a senior Conservative MP has attacked both the Government and the BMA for "losing sight of patients".
Dr Sarah Wollaston, a GP turned MP, said patients had been used as pawns by both sides in the row.
The chairwoman of the Health Select Committee said the planned full walkout of junior doctors at the end of the month will be "disastrous" for patients and put lives at risk.
Junior doctors are objecting to a new contract in England which the Government says will create a truly seven-day service.
They are currently paid more for working unsocial hours at night or at the weekend. But under the proposed new contracts, the Saturday day shift will be paid at a normal rate in return for a rise in basic pay.
The dispute has become increasingly fraught and junior doctors have two strikes planned for this month.
The first will be a 48-hour strike starting at 8am on Wednesday April 6, with junior doctors providing emergency care only.
But strikes planned for April 26 and April 27 will see the full withdrawal of labour by junior doctors - everyone up to consultant level - between the hours of 8am and 5pm on both days.