Walter said the duo would miss a warm-up match against the United States in Mumbai, while top-order batter Finn Allen will also rest as he recovers from a shoulder injury.
"There's a bit of illness in the camp, unfortunately, at the moment, so Devon and Rachin are struggling with a viral infection, which I suppose is part and parcel of touring," Walter told reporters on Thursday.
"Rachin's next door to me, and it hasn’t sounded good all night, so I think he might be struggling."
New Zealand launch their bid for a maiden T20 World Cup title against Afghanistan in Chennai on Sunday.
All-rounder Michael Bracewell missed the recent 4-1 loss to India in the T20 warmup series with a calf injury, but Walter expects him to be fit for Afghanistan, along with Allen.
"Everyone's sort of on track at this stage to be fit and healthy for game one, which is good news," he said.
New Zealand have struggled to build momentum since arriving in the subcontinent, with Jimmy Neesham falling ill and paceman Lockie Ferguson coming back from injury.
While New Zealand lost the final T20 against India this week, Ferguson's two-wicket spell was a bright spot for Walter, with the fast bowler expected to take a leading role in the absence of Adam Milne.
"He has worked incredibly hard to get himself ready for the World Cup," said Walter.
"He said he was going to ease into it, but he was bowling 145 (kph). So if that's him easing in, I'm looking forward to seeing what's to come."