The Ministry for Primary Industries (MPI) has referred evidence of serious staff misconduct to the Serious Fraud Office (SFO), the ministry says.
The evidence came to light as a result of Official Information Act requests from RNZ asking for MPI correspondence with Thompson and Clark.
MPI said in a statement it has also referred the matter to the State Services Commission (SSC) and it was part of the SSC's inquiry into the use of external security consultants including Thompson and Clark.
However, MPI said the conduct of concern did not involve the contracting of Thompson & Clark by MPI.
It said information currently pointed to matters occurring before October 2013, and the staff involved no longer work for MPI.
MPI said it was extremely disappointed, and would make no further comment while the two inquiries were underway.
An SFO spokesperson confirmed to RNZ that "MPI has referred a matter to the SFO" but would not elaborate further.
The SFO has a high threshold for what it investigates - only cases where a number of people are significantly impacted, or if the fraud undermines public confidence in New Zealand as a safe place to invest, is incredibly complex, or has high public interest.
"Measures are already underway internally to understand how the matters may have occurred - even though they occurred some years ago", MPI director general Martyn Dunne said in a statement.
"This will contribute to a 'lessons learned' exercise to ensure they cannot happen in the future.
"We are confident that current processes, structure and culture make it unlikely these events would occur now."
All government agencies will be scrutinised as part of an expanded probe by the SSC into the use of the security firm.
The initial inquiry was announced in March, by SSC Peter Hughes after it was revealed the firm spied on Canterbury earthquake claimants for Southern Response.
The inquiry was further widened to include the Ministry of Business, Innovation and Employment, which had been spying on Greenpeace staff.
MPI said it uncovered potentially serious misconduct by some former staff members in their dealings with the firm. Afterwards the Security Intelligence Service (SIS) also launched an internal investigation after evidence of its staff being unprofessional and biased towards the firm.
And the Department of Conservation used Thompson and Clark to monitor anti-1080 activists since 2016. The department also withheld official information after demands from the security firm, internal emails show.