The herd base charge will increase from €60 to €100 when dairy farmers renew their HerdPlus membership in 2019. For postal customers it will go from €120 to €160.
This follows an announcement last year of a fee increase to the Dairy HerdPlus membership.
"We will be implementing the second and final phase of the increase from 8 February," a spokesperson for ICBF said.
"The €0.50 per cow charge, which was implemented in phase one last year, will remain unchanged and no further fee increases are envisaged for the foreseeable future."
Farmers in the programme received letters last week notifying them of the change and their renewal date.
ICBF is encouraging farmers to use Sire Advice which it said was availed of by 3,800 members last year.
HerdPlus beef farmers escape fee hike