Mr Donohoe said he accepts it has caused “great annoyance and anger” but he also defended the controversial decision.
Two junior ministers or ministers of state are entitled to receive an annual allowance of 16,888 euro on top of their €124,439 salary.
The current Government has three super junior ministers – minister of state for climate and transport Hildegarde Naughton, Government chief whip Jack Chambers and minister of state for agriculture Pippa Hackett.
Mr Donohoe said the decision to top up their earnings was to ensure that ministers of state who are carrying out the same work are paid the same.
“I can absolutely understand the anger that this is causing for some. I’d also make the point that we’re doing that in the week in which we announced a five billion euro stimulus plan for the economy, in which we extended the wage subsidy scheme into next year, and we made the changes to the pandemic unemployment payment over a very long time period,” he told Newstalk.
“We were dealing with a specific matter. We have a number of ministers of state around the Cabinet table that were being paid differently and we were looking to get to a point that if they were doing the same work they were paid the same.
“But all that being said, I do accept that this is causing a great annoyance and anger for some, but I would ask them to just to place this in the context of a huge, huge variety of different measures that we announced last week that are all about getting people back to work and all about growing incomes again.
“The kind of package that we announced last week is the largest package of its kind in the history of our country and it is all about putting in place a response back to the effects of this terrible disease.”
The decision has been widely criticised, with Sinn Fein TD Pearse Doherty saying it is unfair to frontline workers who will receive no pay increase.