Earlier this week, another crossing in Gisborne was painted by Destiny Church members in protest at drag performers reading stories from the children’s section in the public library.
Police confirmed they are investigating the vandalism of the Auckland crossing in Karangahape Rd.
Auckland city central area commander inspector Grant Tetzlaff said police were called at 3.20am today and told three people had poured paint on the rainbow crossing before leaving in a vehicle.
"The vehicle had the registration plates removed and the persons had their faces concealed," he said.
"We have no tolerance for reports of this nature, and when it appears to directly target a particular sector of our diverse community."
Anyone with information can contact police on the 105 number, online using Update My Report, or anonymously via Crime Stoppers on 0800 555 111 using the reference file number 240328/6111.
A spokesperson from Auckland Council confirmed the crossing on Karangahape Rd had been painted over.
Rain overnight washed much of the white paint away, but remnants could be seen.
Auckland Cental MP and Green Party co-leader Chlöe Swarbrick told RNZ's Morning Report programme she was contacted by local constituents and businesses before the sun came up about the crossing.
They were "furious", she said,
"All I can really see here is a sad, bizarre and petty use of energy."
Swarbrick said Auckland Central and Karangahape Rd had a long and proud rainbow history, and it would be cleaned up.
"There's an obvious reason why the person who has done this has decided not to put their name or their face anywhere near what they have done."
Swarbrick expected there to be an "overflow" of support for the rainbow community following this and would end up with "egg on the faces" of those who did it.
"I've had a lot of constituents say this morning that 'they have absolutely no idea who they're messing with'."
She said it was up to political leaders not to participate in this "nonsense" and stand up for these communities.
An RNZ reporter at the scene said the paint had been "slapped" over the crossing. There were tyre prints and footprints through it, and paint had made its way to the footpath as well as along the road.
No one had yet claimed responsibility for painting over the crossing. Destiny Church had been contacted for comment.
Five people were arrested on Wednesday after a group of protesters returned to Gisborne's rainbow crossing with paint cans.
The crossing had been restored after protest group linked with Destiny Church covered it in white paint in opposition to the drag storytime event at the local library.
Hastings District Council on Tuesday cancelled its Rainbow Storytime event due to safety concerns, after councillors and staff received "a large number" of threatening and intimidating messages.