The team confirmed on Twitter that the 28-year-old was suffering from a tight left hamstring and would be left out as a precaution.
With 17 wickets in seven matches at an average of 18.58, Ferguson has been New Zealand's highest wicket-taker in the tournament.
The match in Durham is crucial for England, with a win securing their place in the semi-finals but a defeat leaving the door open for Pakistan.
New Zealand have not qualified for the last four yet but given their superior run rate, Pakistan would need a freak result against Bangladesh on Friday to leapfrog the Black Caps.
(Reporting by Hardik Vyas in Bengaluru, editing by Nick Mulvenney)