Separately, the probe will also look broadly at the use of private investigators by state services.
The expansion comes after allegations from Greenpeace that its staff were being spied on and media reports suggesting the government department had a close relationship with the investigators.
In a statement, MBIE said it had no contracts with Thompson and Clark since 2013, when it hired the company for security risk management services for a petroleum conference.
But it said oilfield company Schlumberger, which runs the seismic surveying ship Amazon Warrior, had provided MBIE with information obtained by Thompson and Clark about an encounter at sea with protesters last year.
MBIE has been prosecuting two people after Greenpeace members allegedly swam out in front of the ship to stop oil exploration.
"The information was obtained by MBIE solely for the purpose of its compliance and enforcement responsibilities," a ministry spokesman said.
The information included the vessels' position, observations and witness statements about the incident.
"MBIE will co-operate fully with [the inquiry] in relation to its engagement with Thompson and Clark Investigations Ltd. [It] has already publicly disclosed details of its relationship."
Southern Response is a government organisation set up to handle claims by people who were insured by AMI.