The workshop informs participants of their legal rights about ending their lives.
But the Council said that Dr Nitschke needs to be registered as a doctor to carry out his euthanasia workshops.
On the other hand Dr Nitschke denies that he needs a licence. He faces a criminal conviction if he's found guilty of the charge.
The workshops were attended by more than 100 members. The Council referred the matter to the Ministry for Health.
The Chair, Professor John Campbell, said that Dr Nitschke was aware of the requirement since 2001.
He was not registered and did not hold an APC. Dr Nitschke said that his legal team would fight the ruling.
He also said that the new series of workshops are very different than the earlier ones, and does not need a medical practioner.
He said that he still comply with the Medical Council's requirements.
He also said that it's been 10 years that he has practiced medicine and if he still does then he himself accepts it to be a criminal offence.
As of now he said that the New Zealand workshops are on hold.