The European Commission called for queries in the Irish Grass Fed Beef PGI application to be addressed before the application can proceed to the next stage.
The letter sent by the EC also addressed Northern Ireland's inclusion in the scheme.
The application for PGI status for Irish Grass Fed Beef was submitted by Bord Bia in November and currently only covers the geographical area of the Republic of Ireland despite industry calls in the north for Northern Ireland to also be included.
In a statement made in response to a query from Agriland, a European Commission spokesperson said: "The Commission has finalised its examination. Ireland has received a letter of observations which it needs to address.
A statement from Minister McConalogue confirmed the changes would be made.
"The European Commission has this week responded to this application with detailed technical queries, which are now being examined," he said.
"At the time the PGI application was sent to the European Commission, I wrote to Commissioner Wojciechowski informing him that Ireland would support the PGI being extended on an all-island basis, when a grass-fed verification system is in place in Northern Ireland.
"The Commission has indicated that this process should be viewed as a non-conflictual ‘amicable procedure’. I am pleased that the Commission has also indicated that it would be available to participate in any appropriate dialogue to assist the process. My department and Bord Bia have been in ongoing dialogue with their Northern Ireland counterparts on these issues since last summer.
"I must emphasise that the PGI application is still under a deliberative process as the European Commission has not finalised its scrutiny of the application.
"I want the PGI for Irish Grass Fed Beef to bring real and tangible benefits to our beef farmers by acting as a way of driving higher values for the world-class product produced by our farm families."
Editor's note: This story has been updated to clarify the EC's position regarding Nothern Ireland's inclusion in the scheme.