Mr Ahern said such a scenario could lead to legal claims against the state, if registrars refused to registrar the civil partnership of same-sex couples.
But the minister confirmed that religious organisations or officials such as priests or vicars would not be compelled to conduct same-sex ceremonies.
At an Oireachtas Committee debate on the Civil Partnership Bill, the minister said state registrars had yet to voice concerns about conducting such ceremonies.
Labour’s Brendan Howlin noted that servants of the state, such as registrars, were obliged under law to carry out their duties.
"You don’t have a Muslim nurse who refuses to serve breakfast if it contains pork."
Mr Ahern agreed, saying that people’s constitutional rights would be breached if civil partnerships were refused under the legislation.
Fine Gael justice spokes-man Charlie Flanagan agreed, noting that, if public servants like registrars refused, "undoubtedly our laws would unravel".
Other officials like bankers, doctors and landlords might then refuse to deal with people because of their sexual or religious orientation.
Mr Ahern also confirmed an amendment to the legislation which will require couples seeking to qualify for certain rights to have lived together for five years as opposed to three. The extended period would rule out vexatious claims by partners seeking redress, such as maintenance, when a relationship ended.
Meanwhile, the Department of Justice yesterday confirmed that the bill would not be expected to pass into law until the end of the year.
It had been hoped the legislation with amendments would pass through the Houses of the Oireachtas before summer.
TDs yesterday also debated the matter of including the words "committed" and "intimate" in the legislation where civil partners may seek redress in the courts.
Concerns were expressed that if a woman leaving an abusive relationship had an affair, she may not be considered "committed" and therefore may be rejected redress under the bill, such as maintenance from her partner.