On Tuesday, the judges in Ljubljana overturned a ban on the option of artificial insemination for single people and women in same-sex relationships.
Parliament must reform the relevant law within a year, the court ruled.
Slovenia's bishops expressed their "regret" about the decision on Wednesday.
"We see this decision as a further step towards dismantling the ideal of the family as the cornerstone of our society," said a statement from the national bishops' conference.
The reality is that not every child grows up in a traditional family.
However, deliberately depriving children of a parent is not the right way forward for society.
The issue has been dividing the south-east European nation for some time.
In 2020, liberal members of parliament pushed through a constitutional review of the ban on artificial insemination for single and lesbian women.
With the ordered reform, "one of the greatest injustices will be corrected", the Left Party in Slovenia commented on the current judgement.