Dr Kardailsky replied that there should not be too many flowering and the heads that emerged were immature.
He said he would have a look the next day and asked that nothing was cut back in the meantime.
The delegated facility operator replied and asked if she could remove flower spikes. He did not reply, so she took photos and removed the plants.
Three days later Dr Kardailsky sent an email to his team leader in which he said he struggled to understand why the officer did that and said it was "malicious, ignorant and bullying".
Two days later an employment investigation was launched.
AgResearch concluded that Dr Kardailsky had breached policy and refused to obey a lawful and reasonable instruction.
The institute said the breach was reported to the ministry and it had deemed there had been an event of "critical non-compliance" where "a major failure in an operation of system that caused, or could have caused a serious risk to biosecurity, the environment, or the health and safety of people and communities".
Ms Ryan said that in Dr Kardailsky's statement of problem he did not seek permanent reinstatement because he was undecided whether he wanted that.
She ruled that the overall justice of the case did not favour granting interim reinstatement.
"The purpose of an order to have an employee reinstated on an interim basis is to preserve the employee's position until his or her claim as to the practicability and reasonableness for permanent reinstatement can be determined."
A full hearing by the ERA is scheduled for December.