Nawaqanitawase, who has won 11 caps for Australia since making his international rugby debut on last year's tour of Europe, will join the Sydney Roosters on a two-year deal from 2025.
The defection of one of their brightest rising stars is a big loss for RA at a time when the code is under increasing scrutiny following a hugely disappointing World Cup campaign.
RA have yet to decide who will succeed Eddie Jones as Wallabies boss, but among the new coach's first big calls will be how to handle the Nawaqanitawase situation in 2024.
"He's not dead to the Wallabies at all. Absolutely not," Waugh told AAP on Thursday.
"I'm just saying we have depth in outside backs coming through."
The code switch will prevent Nawaqanitawase from facing the British and Irish Lions in 2025.
In announcing Nawaqanitawase's impending departure, RA thanked the winger for "his efforts in his 11 Test appearances, as well as for the Waratahs and the Australia Sevens team at the Commonwealth Games".
Waugh said the 23-year-old would be welcome to return to the 15-man code in time for the 2027 World Cup in Australia.
But one complicating factor that could potentially scupper that move is that Waugh last month ruled out the prospect of RA again spending big money on NRL stars.
"I keep talking about being fiscally responsible because the game historically has spent more than we can afford," the chief executive said.
Nawaqanitawase's move follows months of back and forth between RA and the Roosters, who were furious when Joseph-Aukuso Suaalii was wooed to rugby union by the governing body's recently ousted chairman Hamish McLennan.
RA also tried to sign Roosters back-rower Angus Crichton but that move fell over after the Origin forward's camp became increasingly frustrated with the organisation's negotiating tactics.