"The biological father of the child is known to us, and will be known to the child.
"We have agreed with him that his name will not be released to the media."
Wong said the couple had announced the pregnancy because of public interest that would follow due to her ministerial position, but that it was a private matter and that no further statements would be made.
The pregnancy comes as the debate over gay marriage continues to gain momentum.
Prime Minister Julia Gillard has publicly opposed the move, which is against Labor policy, but it is expected to resurface at the party's national conference this year.
Wong broke earlier solidarity on the issue at the South Australian party conference, supporting a motion urging Labor to nationally support the right of all marriages to be recognised and registered by law in Australia, "regardless of the sexual orientation, or gender, of the parties to the marriage".
Gillard yesterday welcomed the news of the pregnancy.
"Penny Wong is a colleague of mine, she's also a very long-term friend so I'm very pleased for Penny and her partner Sophie as they look forward to a new baby and the next phase of their lives, which will be as parents raising a new child," she told reporters.
But Gillard indicated she was not likely to change her view on gay marriage.
"There are strong views in the political party I lead, and we'll have a debate at national conference about those strongly held views.
"I've made my views clear."
Deputy Opposition Leader Julie Bishop congratulated the couple.
"The birth of a child is a cause for great happiness for Penny Wong and her partner," she said.
"I wish them all the very best in the coming months."
