"We are going to try and keep going with just the sport jumping and student side of it, but it's going to be a big problem," spokesman Doug Telfer said.
"The tandems ... was what kept the club running and now that we've lost that, it's going to be pretty difficult."
Mark Horning has put his Matamata-based Skydive Waikato operation on hold but has gained certification for his Fox Glacier business.
"With the aircraft being maintained by different maintenance providers in different areas, we elected to focus on the Fox Glacier operation and put Matamata on hold until we see where everything goes," he said.
The decision had been mainly driven by the rule change.
"I've sweated bullets over the last couple of months trying to get it all in line."
John Martin of Tauranga Tandem Skydive said his company was having to re-submit its application, but expected to receive certification within the next few weeks.
"I'm sure there will be other businesses suffering big time and other businesses simply won't be able to cope, purely because of the paperwork you have to put into it, the bureaucracy and the huge cost that goes with it."
Skydive Abel Tasman owner Stuart Bean was aware of closures of a handful of skydiving operators.
He had taken the rule change seriously enough to hire another worker to help gain certification, ultimately costing him between $40,000 and $50,000.
Despite more than four months of work and getting his application in on time, his company was accredited only hours before the deadline.
Mr Bean believed many operators had underestimated the time and cost involved in the process.
"I think a lot of the operators thought they would be able to chuck in a bit of stuff just before it was due, but it was a very extensive process."
CAA spokeswoman Emma Peel said just one skydiving firm had submitted its manuals by the recommended deadline of February 1.
While the rules would have been a "big step up" for some businesses, she didn't see it as a case of their being forced to close down.
"They're not having to close down - they've decided actually that the leap from hobbyist to professional is too big for them to take - and you've got to bear in mind these people have essentially been earning money off passengers without providing the kind of safety standards a passenger should have the right to expect."