The outside back was a late withdrawal last Friday against his former team Queensland due to an outstanding relocation fee owed by the club.
The debt wasn't settled before the Rebels went into voluntary administration and while Rugby Australia (RA) have guaranteed the players' contracts this season and put the coaches on short-term deals, this payment falls outside of that.
The future of Melbourne in the competition rests in the hands of RA, with the club in massive debt.
Daugunu, who played for Australia A last year and has seven Test caps, was back at training on Tuesday but too late to be considered for the Hurricanes match in Palmerston North, with the team departing Wednesday.
"It's between him and his agent and Rugby Australia and they've been trying to work it out," Rebels coach Kevin Foote told AAP.
"Filipo actually came to training today which is great - he's not up for selection this week because it's too late as we've already finished our training week but just to have him back is very pleasing for us."
Suffering a heavy loss to the Reds, Foote said post match they had a poor preparation without alluding to Daugunu, with the club stating his absence was for "personal reasons".
They are currently seventh with two wins and two losses with Foote and his assistant coaches trying to keep the distraction of an uncertain future at bay.
RA boss Phil Waugh told AAP on Monday the decision on the survival of the club was taking longer than he would have liked.
"No news is not good news in this scenario because you actually start living in the future and that's not good either," said Foote, who was re-signed on a four-month deal when RA took over the club in the pre-season.
"You start worrying about things you don't know anything about.
"There's only three pay cheques left and when you think about that it's very concerning.
"But the last thing I want is that they tell us that we're not going to be around because then there could be a mass exodus or people thinking about jumping off.
"We're still in the belief that we'll be around and we can keep this group together because it's a very talented group and we can do good things."Â
