The ballot of members of Unite showed 94.8% of the chaplains, health visitors and other NHS staff were opposed to the deal.
However the pay rise is likely to be in pay packets next month because it was accepted by the RCN and Unison, which negotiated the deal.
Unite assistant general secretary Gail Cartmail said: ‘Our members are angry and frustrated that they are being asked by the government to accept this woefully inadequate three-year pay deal.
‘Unite members believe this pay deal is in effect a substantial cut when you take into account the inflationary trends in the economy.’
Unite’s 12,000 ancillary and ambulance staff also rejected the pay deal in a separate ballot last month.
Midwives represented by the RCM and NHS members of the GMB have also rejected the deal.
Read more on this story in next week's NT.