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Tennis New Zealand confirmed the former Dunedin-based coach's resignation on Friday, just under 15 months after he was appointed to the role.
It's a curious situation, as, unlike some previous coaches at that level, Carter is universally admired and respected by the female players.
He has built strong relationships with Paige Hourigan, Valentina Ivanov and Erin Routliffe and has put much of his own time — outside his contracted 70 days a year — into helping Kiwi players.
And the Fed Cup team seemed on the verge of a bright future, with Ivanov and Hourigan showing potential in singles and Routliffe making great progress in the doubles arena.
But Carter has walked away from a role he has aspired to for much of his long coaching career.
However, Carter was reluctant to elaborate on the reasons for his departure.
"I don't really want to comment," Carter told the Herald.
"I just feel this needs to be dealt with internally, initially. There are clearly issues — I am not going to lie — and some far-reaching ones but I want to see how the next few weeks pan out. Hopefully, there will be some steps forward and my successor won't need to face the same issues."
Carter, who spent 14 years overseeing tennis development in Dunedin, bringing through the likes of WTA professionals Dianne Hollands and Shelley Stephens, before a decade-long stint in England running his own academy, admitted it was a wrench to leave the programme.
"It's a role I have worked all my life for, and I had almost given up on the chance of taking it," said Carter.
"I've loved the job...so to feel like I have to resign is quite sad. But I will continue to help the players as much as possible — nothing changes from that point of view — it's just that I am no longer Fed Cup coach."
Tennis New Zealand CEO Julie Paterson said Carter's decision to leave, while unfortunate, was a personal one.
"Neil has been very committed [to the team] and has supported them in making some good progress in a pretty short time [so] it is disappointing," said Paterson.
Paterson was positive about the future direction of the women's programme and didn't feel there were any underlying problems.
"No, I don't think so," said Paterson.
"We have made good progress with the women's team and they are really well connected with Christophe [Lambert, national performance coach] and Simon [Rea, Tennis NZ high performance director]. We have got quality coaches in our programme, it's just a shame that Neil felt he couldn't continue with it.
"Neil has done some really good stuff and we recognise his commitment, passion and engagement with the team which has been fantastic, but he is not doing it on his own. He is part of a wider team. I believe we are heading in the right direction."
Tennis NZ will begin the search for a replacement immediately, ahead of the Asia Oceania Group 2 tournament in June.