Minister for Health James Reilly has said hospitals must meet maximum waiting times for inpatient and outpatient procedures by mid-year.
The Health Service Executive was also told it must maintain these targets throughout the second half of 2014.
In a letter to HSE Director General Tony O'Brien, Mr Reilly said he is concerned that the past focus of achieving a specific target by the end of the year "is not properly incentivising some hospitals" to manage their waiting lists all year round.
It means there will now be an eight-month maximum waiting time for inpatient procedures and a one-year maximum waiting time for outpatient procedures by mid-year and hospitals must maintain the targets to the end of the year.
Due to capacity issues with orthopaedics and ear, nose and throat procedures, the target for these specialties is a maximum one-year wait by the end of 2014.
In 2015, hospitals will have to meet a six-month waiting list target for inpatient procedures during the first half of the year and maintain that and a nine-month target by mid-year for outpatient procedures and maintain that to year end.
The letter, seen by RTÉ News, says that in 2013, patients were enduring long waiting lists in the middle of the year and an intervention fund was required to reduce the waiting lists by the end of the year.
The minister said he was concerned that the hospitals that did not follow best practice in waiting list management had their problems resolved for them by the intervention fund.
He has told the HSE that in the future waiting lists must be met by reforming how hospitals operate and not by providing extra funding where they fail to follow best practice.