"She unfortunately sustained a sprained ankle the other day, so we will be accessing her later today and just checking to see were she's at," Southby said.
"We've just been mulling over a few options but at this stage a decision won't be made until later today."
Fakahokotau's injury comes just days after Kayla Cullen was ruled out for the series with a knee injury.
Southby said the exclusion of yet another defender meant that the anticipated debut of uncapped Fern Michaela Sokolich-Beatson could "potentially" be sooner than expected.
"We are looking at all of these games over the next couple of days to make sure that we do give people opportunities and I guess for her [Sokolich-Beatson] it may come sooner than it was going to," said Southby.
"It's never ideal but we know about them and at this stage we can make adjustments to them … were doing everything that we possibly can to make sure that players are in the right space."
Claire Kersten and Maia Wilson were called in as cover for the four-day Taini Jamison series, with shooters Ameliaranne Ekenasio and Maria Folau both managing injuries.
Ekenasio, who was recalled into the national team after taking time away from the game, suffered a finger injury, while Folau continues her comeback from a knee complaint.
None of the players have yet been ruled out of the Commonwealth Games.
The Silver Ferns will open the series against Malawi tomorrow night at the North Shore Events Centre.
Silver Ferns squad: Katrina Grant (captain), Maria Folau (vice-captain), Ameliaranne Ekenasio, Temalisi Fakahokotau, Shannon Francois, Kelly Jury, Grace Kara, Claire Kersten, Bailey Mes, Te Paea Selby-Rickit, Samantha Sinclair, Michaela Sokolich-Beatson, Maia Wilson
