A message board printed with the words "all lives matter" at the St Patricks Catholic Church in Masterton appears to have been partially vandalised, with letters now hanging off it.
It comes after a weekend of rallies in Auckland, Wellington and Dunedin, where thousands of people turned up to show their solidarity with the Black Lives Matter protesters in the United States.
There has also been growing unrest in the US at the weekend, after a black man, Rayshard Brooks, was shot dead by police at a Wendy's drive-thru in Atlanta, after he attempted to run from them with one of the officer's tasers.
The Masterton church has not responded to RNZ's requests for comment, but the Archbishop of Wellington - Cardinal John Dew - condemned the "all lives matter" sign.
In a statement, Dew said the sign was put up without the knowledge of the parish priest while he was away on leave.
"As Archbishop for the diocese, I do not support the placement of that sign. It should not have been put there.
"A church should not be politicised this way. A church should be a safe space for everyone, a place where everyone feels welcome without being confronted with politicised material that some could find unwelcoming or offensive."
Masterton Mayor Lyn Patterson said the church did not seem to have been aware of the controversy surrounding the "all lives matter" slogan.
"I have spoken to the church about the message that was on the board outside the church and I'm really comfortable that the message wasn't intended to undermine the Black Lives Matter movement," she said.
"I just don't know whether they had realised the full on consequence of what 'all lives matter' was in regards to the Black Lives Matter movement."
She said the message was linked to the feast of the corpus christi religious celebration.
"It is a Catholic commemoration or celebration which was actually over the weekend, and the intention was to celebrate the humanity of all people," she said.
Patterson said she had not heard much from the community about the message.
"I haven't had any phone calls around it but I would understand and certainly appreciate why people might feel strongly about the signage, which is why I popped in and had a discussion with the church.
"Lots of people have individual views on it, from my perspective, at the moment the 'all lives matter' messaging against the Black Lives Matter movement - it's just not appropriate timing.
"We respect all cultures, we consider ourselves an inclusive community, but we also respect that the timing for them to put that message up may not have been the best time."
The mayor was not sure if the sign had been taken down, but said she would not be asking the church to remove it if it was still there.
RNZ