Kirker said he did not have any plans to discuss the matter with the media, and also had not suggested anybody in the Labour Party do so.
"I want to say sorry if my previous email was perceived as a threat," he said.
"I was just trying to say that your policy could mean that there would be people that were unhappy about its implications.
"It was a poor choice of words on my part and I can see how it could be perceived as a threat."
Kirker said he was not after a free stand, but rather a walk through the market.
"I was told over the phone if Jacinda walked through the market with Labour logo without paying $500 on any occasion, she/we would be removed," he wrote.
"This was, and remains, concerning to me."
The company running the night markets charge between $300 and $500 for parties wanting "exclusive" campaigning on any given night.
Kirker was told Ardern could not campaign on the date he wanted because the National Party had already booked a spot.
Market owner Paul de Jonge said the decision to have "exclusive rights" for a single political party to campaign on any given night was because parties that campaigned at the night markets before the last election were "disruptive" to business.
The cost to political parties, which is about double that of food stalls, includes a prime double spot with table and chairs, and all-night access for party members to mingle with the market crowd.
The company runs night markets in Mt Wellington, Botany, Henderson, Papatoetoe, Pakuranga and Glenfield.
