The ad for the new Hilux will stop screening immediately, the company announced on Sunday.
Toyota New Zealand boss Alistair Davis says the decision hasn't been taken lightly and reflects feedback from members of the public.
"We apologise unreservedly for any offence we have caused. We've listened and we'll stop screening the ad," he said.
"The public and in particular Toyota's customers are the cornerstone of our business and we've been closely monitoring the ad's response and felt the groundswell of detractors was growing."
Karyn Hay talks with Hans Kriek from SAFE about the outcry
Mr Davis said the company never intended to cause offence.
"The audience we were hoping to positively engage with this story is unlikely in our view to share the opinions of those we have offended, and are likely to see the ad as being a computer-generated exaggeration of real life meant to be amusing rather than shocking," he said.
"That was unquestionably how we envisioned the advertisement being received.
"However, some viewers are genuinely worried about the message the advertisement sends, and so for that reason we have decided to stop screening it."
The ad shows several CGI animated animals seemingly happy to be hunted and fished then transported on the back of the new Hilux.
Toyota New Zealand says all the animals in the ad are regularly and sustainably hunted and fished.
The ad also features a possum, a common pest.