The Ministry for Primary Industries has referred evidence of "serious staff misconduct" to the State Services Commission (SSC).
Martyn Dunne, Director-General of the Ministry for Primary Industries, said MPI is "extremely disappointed by the nature of the potential misconduct."
He confirmed it is part of the SSC's inquiry into the use of external security consultants, including Thompson & Clark Investigations Limited.
The matter incidence of serious misconduct "did not involve the contracting of Thompson & Clark", Mr Dunne said.
MPI says evidence suggests the alleged misconduct occurred before October 2013. Staff involved no longer work with MPI, Mr Dunne said.
"Measures are already underway internally to understand how the matters may have occurred even though they occurred some years ago. This will contribute to a 'lessons learned' exercise to ensure they cannot happen in the future," Mr Dunne said.
"We are confident that current processes, structure and culture make it unlikely these events would occur now."