Dozens of trusts face compensation payouts and a temporary ban on recruiting overseas staff because they are not on an official Home Office immigration register.
The deadline for employers to apply to sponsor workers from outside the European Economic Area passes next week, but only 12 trusts and primary care trusts are listed as registered.
Employment lawyer Duncan Bain of Morgan Cole said workers may be eligible for damages if they are unable to extend their visa due to their employer failing to register as a sponsor. This could result in trusts paying out thousands of pounds in compensation.
Widespread confusion about the "ambitious" changes sprang from the fact that it gave human resources teams a vastly expanded role in immigration processes for workers, Bain said, adding: "There will be some trusts where a very significant proportion of staff will fall under this regime."
The new points-based system comes into force on 30 November but organisations have until 1 October to apply to be sponsors.
NHS Employers head of programmes David Grantham said: "Employers need to get applications in early because it may take some time to process them.
"If they leave it too late, it may take longer and there may be a gap during which they're not allowed to recruit."
A Home Office spokesman said that the points-based system introduced "one of the biggest shake-ups to the immigration system in a generation". He said: "Our message is loud and clear - if you want to employ foreign workers from outside the EEA, you need to apply now for a sponsor licence."