Just 60 of the 280 junior doctors recruited from India and Pakistan to ease the manpower crisis in hospitals have secured the green light to work.
There have been delays in registration with the Medical Council due to doctors not supplying supporting documentation and delays in the Health Service Executive providing other material.
Over 30 doctors also failed the clinical skills examination.
The HSE must supply declarations for the doctors, confirming they have been offered a specific post, provide a copy of their contract and confirm that they will be supervised.
The Medical Council says these have been supplied in half of the cases.
The HSE says that the delay in the junior doctors starting has put pressure on the service and that other doctors are having to work longer hours to ensure the system copes.
All 280 doctors have been living in Ireland since around July, with the majority still waiting for registration and appointment to a hospital post.
The HSE said the registration process is complex and that the Medical Council amended the required HSE documentation in late August.
The executive said that the vacancy levels will reduce signifiantly as the doctors now here are registered and become available.
The HSE is funding their accommodation at a cost of €100 a week for eight weeks per doctor.
The doctors are living in bed and breakfast accommodation or hostels, while others have hospital accommodation.