The EU chief executive says the Union should move to a system of majority voting, and scrap national vetos on tax.
In his State of the Union address Jean-Claude Juncker also discussed Brexit, and assured that all member states will continue to show solidarity with Ireland when it comes to the border with the North.
Irish MEP Brian Hayes has warned that any changes to the EU voting rules on tax would have detrimental effects for Ireland.
"President Juncker’s comments on changing the EU voting rules on tax matters in the European Council must be blocked at all costs," said Mr Hayes.
"The European Council currently votes on tax matters by way of unanimity, thus allowing any country big or small to veto an EU tax proposal.
"The EU Treaties make it absolutely clear that tax decisions are taken by way of unanimous vote.
"The only way this can change is by further Treaty change but this is something that Ireland cannot go along with."
However, Jean-Claude Juncker says any changes would be for the greater good of the European Union.
"When we act together, the European Union can achieve results
"We must show that Europe is able to overcome differences between north and south, the east and the west, the European Union and Europe.
"We have to show clearly that together - east, west, south and north - we are able to plant the seeds of a more sovereign Europe."