The Health Service Executive went over budget by €132 million in the year to June, according to its latest performance report.
The overrun represents just under 2% of its budget for the year of nearly €14 billion.
The April-June report says that around €33 million of the overrun is due to the early restoration of the Lansdowne Road Agreement.
A further €21 million relates to historic accelerated income targets for acute hospitals and demand-led services are also contributing to the overrun.
Mr Varadkar said funding had increased by more than a €1bn over the past two years to bring spending on health to its highest level in the history of the State.