Twelve military personnel are launching a legal challenge to the directive that would see them discharged for declining a Covid-19 vaccination.
The group has filed an application for a judicial review of the directive.
A statement from their barrister said they were standing up for their fundamental freedom to decline medical treatment.
Barrister Christopher Griggs said in the past it had been very rare for vaccination status to be used as a ground for discharge from the armed forces.
The group's application was founded on the claim that the chief of defence force must follow a statutory process before taking action against personnel, Briggs said.
The directive was unlawful and breached the group's right to refuse medical treatment under the Bill of Rights Act, he said.
But retired law professor Bill Hodge said it would be difficult for the Defence Force personnel to convince the courts they did not have to get the Covid-19 vaccine.
The wellbeing of the greater good had often justified limitations on individual rights, Hodge said.
It would be helpful to have the argument tested in the higher courts, he said.
A Defence Force spokesperson said as the matter was before the courts it could not comment.