It has urged the HSE and Department of Health to take part in urgent negotiations.
Junior doctors working for the HSE have voted “overwhelmingly” in favour of industrial action in relation to long working hours and unsafe conditions.
This means patients could face another round of cancelled operations, following strike action by medical scientists in recent weeks.
The Irish Medical Organisation (IMO) has balloted 7,500 doctors in recent weeks, and on Monday said 97% of the votes by the time the ballot closed were in favour of taking action including a possible strike.
Non-consultant hospital doctors say they're prepared to strike if unsafe and illegal working hours aren't addressed.
The union is seeking urgent talks as more and more junior doctors are opting to leave the country over long hours and toxic working environments.
It has called on the HSE and Department of Health to take part in urgent negotiations, and said if this does not happen they will serve 21 days' notice for some form of industrial action.
"This ballot result clearly demonstrates the determination of NCHDs and, while any kind of strike action is extremely difficult for doctors, there may be no choice," said Dr John Cannon, Chair of the IMO NCHD Committee.