The HSE has referred the decision by the Irish Medical Organisation to take industrial action over long hours worked by non-consultant hospital doctors to the Labour Relations Commission.
Both sides met today to discuss contingency measures.
The IMO expressed dismay at what it claims was a failure by the HSE to table settlement proposals.
The HSE says it is seeking an early date for talks at the LRC.
NCHDs are due to hold a one-day national strike on 25 September, followed by rolling action in each of the HSE's four health regions.
The IMO has promised that emergency services, oncology and dialysis will not be affected.
The HSE has said that many large hospitals have made significant progress towards compliance with the European Working Time Directive on a 48-hour-week for doctors, but there are problems in small to medium sized facilities.
The strike over working hours follows an IMO ballot of NCHD members in which 97% of 1,000 doctors voted for action.
The IMO represents around 2,000 of the 4,800 junior doctors in the health system.