The archaeological excavation work at Carrickmines Castle in south Co Dublin, which has unearthed important medieval remains, is due to conclude at 5 p.m. today.
However, agreement on how best to preserve the remains has not been reached between An Taisce and the National Roads Authority.
The Green Party has accused the Minister for Transport, Mr Brennan, of failing to protect the site.
While initial proposals from the National Roads Authority to preserve key aspects of the castle, situated in the path of the M50 motorway, were welcomed by An Taisce, they were not sufficient to secure the heritage body's full support.
In its response to the NRA proposals, An Taisce has said it acknowledged that the motorway should "sadly" proceed, but it argued that there were no valid reasons why subsidiary elements, such as an access road, could not be moved and a roundabout reduced in size.
Addressing the National Roads Authority proposals in detail An Taisce said:
The upstanding remains as defined by the NRA for preservation consist of a remnant of a gatehouse measuring 3.5 metres by 4.2 metres.
The 50 metres of fosse, a defensive structure, which the NRA proposes to retain is part of a feature which is 237m long.
There are no proposals to retain the remains of any of two outer fosses, a medieval water mill, three kilns, houses, a moat or workshops.
The proposal to retain a medieval wall on a roundabout, involves just 50m of a 237m wall which currently survives.
According to An Taisce, the destruction of the masonry structures would directly contravene the Government's own "Framework and Principles for the Protection of the Archeological Heritage", while the "deliberate non-recovery" of archaeological objects would contravene the National Monuments Act.
The organisation also said it was ironic that the dig was being ended at the same time as the State was launching National Heritage Week.
Meanwhile, Mr Brennan has said he will decide next week on any amendments to the original scheme, after he has studied the submissions from the NRA and An Taisce.
A spokesman for the Minister also pointed out that the ending of the dig was the "end of a natural phase".
But it did not mean that anything detrimental would happen to the site between now and the Minister arriving at his decision.
Some €6 million has already been spent on the dig which has lasted in excess of one year. The numbers employed on the archaeological team averaged between 20 and 30.
An Taisce, Friends of Medieval Dublin, and Fénechas - the Brehon Law Project - are to host a number of events, including a public meeting at the Walton Theatre in Trinity College at noon today, which will discuss the archeological, historical and legal aspects of the controversy.
There will also be a series of "Concerts for Carrickmines" at the Temple Bar Music Centre, Dublin, on September 5th and 14th, hosted by Rónán Ó Snodaigh.