Johns agreed there was initially some bitterness about Jones crossing the ditch, but this sentiment didn't last long.
"There's been a reasonable amount of money invested in Sacha's career," he said.
"But we quickly realised that she's a professional athlete and, yes, while we'd like New Zealand to feature in her plans, at the end of the day she's looking after the best interests of her career.
"She believes - and rightly so - that she can get better assistance playing under the Australian flag."
Part of that assistance includes the possibility of wildcards into more lucrative Australian tournaments, travel and accommodation subsidies as well as a full-time travelling coach.
"That's certainly something we can't afford in New Zealand," Johns said. "And just being in a programme that has far more depth than the New Zealand programme has at the current time."
Jones' world ranking of 274 will see her become the tenth-ranked women's player in Australia - a country with a deep pool of talent in which the 21-year-old will now be a small fish.
"But, I guess, it's just that extra support she will have when she's out touring the world at various tournaments around the place trying to earn more ranking points," Johns said.
"Although she's not ranked No 2 [in Australia, as she is in NZ] she will certainly have far more access to resources in the Australian programme than she would in New Zealand.
"Tennis NZ is never going to be able to compete with the resources that Tennis Australia has. They have a Grand Slam and they earn tens of millions of dollars each year from that Grand Slam."
Johns refuted the idea Jones' departure from her home country was an indictment of tennis in New Zealand, preferring to think of it as an isolated case.
"She's in a reasonably unique position in that she does have duel citizenship, so it's easier for her to make the switch," he said.
"Unfortunately the reality is, like a lot of professional sports in New Zealand, the grass is greener on the other side of the fence and some of our athletes are going to go."
Johns added his organisation would leave the door open for Jones if she were ever to return to New Zealand.
"She's a Kiwi at heart. If it doesn't work out for her in Australia then, absolutely, we'd welcome her back with open arms.
"If it does work out over there and she achieves her goals and goes onto great things then, rest assured, we'll be claiming her as a Kiwi forever and making it pretty clear that this is where she got her start."
Jones will play in January's ASB Classic in Auckland where she has been awarded a wildcard. Following that tournament, she will travel to Australia where she is in line for a wildcard into the Australian Open.