Speaking at St John's Cathedral in Limerick, the Primate of All Ireland said the measures would hugely change peoples' concepts of the family.
The Civil Partnership Bill, which was published in June, will for the first time mean that same sex couples will be recognised as partners before the law and will be treated like married couples for tax and social welfare when registered.
In his homily, Dr Brady said marriage between a man and a woman will always remain the ideal environment in which to raise children.
He said any government which undermines such an environment could hardly be said to be promoting the common good.
Cardinal Brady also said those who refuse to officiate at a same sex wedding would be guilty of offence and described this as 'an alarming attack on the fundamental principle of freedom of religion and conscience.'
He said the legislation leaves the door open for individuals and religious organisations to be sued in a variety of ways for 'upholding their belief that marriage is an institution exclusively for men and women'.
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SIC: RTÉ