The country star is scheduled to play five sell-out gigs at Croke Park from 25 to 29 July, but the council has ruled that two cannot go ahead.
Brooks responded by stating it will be a case of "five shows or none" - however, in a statement on Friday evening, the council said the decision it has made cannot be amended.
It moved to clarify the grounds on which it had refused permission for the concerts and said it had expressed its concerns during a number of prior meetings with the promoters.
The council said: "Dublin City Council has been consistent (since it was confirmed that tickets were sold for five concerts) in informing the promoter and his agents that its main concern was the impact that five consecutive concerts would have on the local area.
It should be noted that event licence decisions made under the Planning & Development Acts cannot be amended or appealed.
Dublin City Council
"As the licencing authority, Dublin City Council must adhere to the procedures laid down in the attendant planning act and regulations.
"The decision to grant or refuse an event licence is made by senior management in DCC's Planning Department, to whom those powers have been delegated by the chief executive."
Meanwhile, Garth Brooks fans across the country have been left waiting to see what will happen.
One fan told U105: "Why let people queue for hours in the rain to get tickets, to book hotels, (where) the prices went sky high, now we are left with tickets (that may be) no good.
"It's not fair on the people who have paid their money. My poor son stood in the rain for me to get those tickets."
Dublin City Council has only granted permission for the concerts on Friday 25, Saturday 26 and Sunday 27 July, refusing permission for the concerts on Monday 28 and Tuesday 29 July.
A statement issued from the US by Garth Brooks on Thursday evening said: "I can't thank the people of Ireland enough for how welcome they have made me feel.
"I have faith Dublin City Council will make the best decision for the people of Ireland.
"For us, it is five shows or none at all. To choose which shows to do and which shows not to do would be like asking to choose one child over another."
However this plays out, Ireland has my heart and always will.
On Thursday, a statement from Dublin City Council said it would not be appropriate to grant five consecutive nights of concerts at the GAA venue, considering three consecutive One Direction concerts have already taken place from the 23 to 25 May.
It added: "Given that Croke Park is situated in a heavily populated residential area, five shows in a row following on from the three concerts already held there this year is considered an over intensification of use of the stadium for the holding of special events/concerts.
"It would be in effect permitting an increase of 100% in terms of the maximum number of concerts that had previously been held in Croke Park in any given year since the redevelopment of the stadium."
The council said they also took into consideration the "cumulative effect on residents and on some businesses" in the area.
On Friday Aiken Promotions released a statement clarifying they had "followed the licensing process as laid down under the current regulations" in relation to the gigs.
They said it was "standard practise" to inform the licencing authority, then to announce an event and to put the tickets on sale before an application is submitted.
The promoters said they submitted an application for the events 14 weeks before the first concert. Current regulations require that this must be done 10 weeks in advance.
Irish Minister for Transport, Tourism and Sport, Leo Varadkar, said: "This is a blow to fans and to visitors coming from abroad. The way this happened at the very last minute is clearly unsatisfactory from everyone's point of view and highlights the need to review the major events licencing laws. Nonetheless residents have legitimate concerns about five concerts in a row which the GAA has conceded was a mistake.
"The decision on the licence was made by Dublin City Council and there is no provision in law for it to be appealed or overturned other than by the courts.
"There were only supposed to be three concerts when the tour was first advertised and I see no reason why these should not now proceed. The onus is on the promoters to ensure that two other concerts are rescheduled or relocated."
More than 400,000 tickets for the gigs have been sold.