Spin Master, the US company which makes the toy, has sold out but said it would be restocking soon.
The company first hinted at the shortage earlier in the month saying it had almost sold out.
"The consumer response to Hatchimals has been extraordinary, exceeding all expectations," the company said.
"Some of our first shipments have already sold out. While additional product will hit retail shelves in November, we anticipate this inventory will also sell out quickly."
Spin Master said it had increased production and would have a new batch ready for early 2017 but the limited supply has already been felt globally with the toys sold out across most stores in New Zealand.
Stockists including The Warehouse which was selling the toy for $88, have reported waitlists for the toy and auction site Trade Me has been inundated with listings for Hatchimals.
Trade Me's Logan Mudge said demand for the toys had sky rocketed particularly in the last week, with 58 per cent more sales of the product than the previous three weeks combines.
He said searches for the toy had also jumped 245 per cent since the same time last week.
"We knew that Hatchimals were popular but we hadn't foreseen a nationwide shortage of them a month away from Christmas," Mudge said.
"There have been a few rumours around Trade Me that entrepreneurial parents have decided they could make a little extra Christmas cash by putting a Hatchimal they bought earlier in the year up on site."
"It's certainly not a silly idea given the activity we're seeing."
Spin Master said it would continue to update its site as more Hatchimals became available, saying it didn't want customers to be disappointed.
It also said it did not support inflated prices from non-authorised sellers but this hasn't stopped users cashing in.
There are currently 52 Hatchimal listings on Trade Me with buy now's of up to $300 and more than 100 watchers on some listings.
The highest selling Hatchimal to date on the site went for $295 but Mudge said this may go up as it got closer to Christmas.
Callum Irvine is one customer that has bought up several Hatchimals to sell on Trade Me. The Thames father-of-two said he saw the trend coming and began stocking up.
"It was late October when I noticed on social media, people were starting to say they were disappearing fast off the shelf," Irvine said.
"So I started importing some of them from overseas and then that dried up so I got a few local ones as well. I've sold about eight to ten for on average about $250. They're all $1 reserve so it's just whatever people are willing to pay."
Irvine said he had sold one yesterday for $285 and had several more on Trade Me with current bids of between $98 and $160.
What are Hatchimals?
The toys have been described as a Furby inside an egg. The "magical creatures" interact with kids while inside the egg, which contains one of two interactive Hatchimals. Kids need to take care of the Hatchimal while it is inside the egg to get it to hatch. When the rainbow eyes appear, the toy will hatch, pecking its way out of the egg while singing 'hatchy birthday' to itself. Once the toy has hatched, the owner needs to raise it from baby to toddler to kid. Hatchimals can learn to walk, dance and play games, and can repeat what you say in its own voice. Videos of Hatchimals hatching have gone viral on Youtube and boosted demand for the toy.
