"We've had a discussion about [it] and as I said to her, had I known this was where it was going to land up I wouldn't have got involved," Hipkins said.
"I had no intention of getting involved in Australian domestic politics."
Hipkins, who has a keen interest in the rights of Kiwis living in Australia, said he asked the citizenship question out of personal interest.
A spokesman for Internal Affairs Minister Peter Dunne says Australian media had also lodged specific questions about Joyce at or about the same time as Hipkins' general question.
The requests had led to Joyce being informed, he said.
Joyce is the fifth Australian MP to have their citizenship questioned since last month, after senators Scott Ludlam, Larissa Waters, Matthew Canavan and Malcolm Roberts.
- NZN