"It's not a good look for the whole Parliament and it is embarrassing for the whole Parliament - no question there," Hipkins told Newshub's The AM Show.
He said he responded to the "Opposition threat".
"The Prime Minister was very clear that she did not want a vote, and so I had to move quickly. So, yes, we did have to compromise."
Hipkins said he thought there had been an understanding in which National would not contest the Speaker position and Labour would not contest the Deputy Speaker position.
He was taken by surprise when National indicated that they might challenge the nomination.
"That's a matter for the Opposition. They chose to disrupt. That's their call.
"We didn't have all of our MPs sworn in. They will all be sworn in fairly shortly, and then it will never be an issue again, because we will have our full voting strength."
This morning is the State Opening of the 52nd Parliament. Governor-General Dame Patsy Reddy will read the Speech from the Throne, outlining the Government's intentions for the parliamentary term.