He said it made "no logical sense" that individuals who are gay can adopt, but not those who have entered into a civil partnership.
Speaking about lesbian, gay, bisexual and transgender (LGBT) parenting at a conference organised by the Marriage Equality organisation yesterday, he acknowledged that joint adoptions were currently limited to married couples.
"It makes no logical sense, in circumstances in which an individual who is gay can individually adopt, and that a couple in a civil partnership should not be able to adopt," he told the delegates at the conference in the Royal College of Surgeons in Dublin.
Mr Shatter said the bill on family reform that he was working on "aims to put in place a legal architecture to underpin diverse parenting situations".
He is expected to have this bill ready for Cabinet consideration later this year.
"It seeks to provide legal clarity on parental rights and responsibilities in such situations," the minister said.
"What I am aiming to do is to address the diverse situations of LGBT parents but also of heterosexual parents whose situations are not adequately addressed under the current law."
Mr Shatter also referred to international research during his address, and said that there was "no one family form which has a monopoly in terms of cherishing a child".
He pointed to research from America which, he said, "reminds us that the key to child welfare is good parenting rather than a specific family form".
He described the Government's decision to hold a referendum on same-sex marriage as a "major step forward".
However, Mr Shatter highlighted the need to advance the issue of children and parental rights before the referendum takes place next year.
"The objective of the bill is to remove the legal inequalities between children in a large range of non-traditional families relative to those living in a constitutional family based on marriage," he said.
Amongst the delegates at the conference who hope to see clarification of rights for same-sex parents was Dr Angela O'Connell.
The Cork woman has two sons, aged 11 and seven, from a same-sex partnership and is upset about the laws regarding her family.
Dr O'Connell's 11-year-old son came into her life as a foster child, and her partner adopted him, while her younger son was born to her partner.
"They don't have legal relationships to any of the people in the family that they have grown up in on my side.
"They are not aware of it, and we don't make an issue of it because to us it's love that makes a family, even though we know that it's law that makes a family in the eyes of the State," she said.
Dr O'Connell, who has since split from her partner, shares equal custody of her children.
Her message to the minister was that the new legislation "has to put the children at the centre".