All government agencies will come under scrutiny as part of an inquiry into the use of the security firm Thompson and Clark.
The Security Intelligence Service has also launched an internal investigation into its dealings with the controversial security firm.
The inquiry was further widened to include the Ministry of Business, Innovation and Employment, who had been spying on Greenpeace staff.
Today, Mr Hughes announced that the inquiry would cover all government agencies.
He was concerned about what had surfaced in the inquiry to date and new information available about other agencies.
The fresh material came to light in official information requests from RNZ to the Ministry of Primary Industries and the Security Intelligence Service.
SIS launches internal investigation
The SIS is also looking at its dealings with the firm, with OIA information released to Checkpoint this afternoon showing SIS director general Rebecca Kitteridge has concerns about the professionalism of her staff and whether they were biased towards Thompson and Clark.
Ms Kitteridge was concerned by the tone of emails sent between one staff member in the SIS protective security requirement team and Gavin Clark from the security firm.
The emails showed the staff member and one of the directors of the firm were old friends who met regularly, and appeared to show Thompson and Clark were using the friendship to book contracts with government agencies.
MPI misconduct uncovered in request response
The other OIA request was for all correspondence received by MPI from Thompson and Clark for the past eight years.
MPI said the misconduct was uncovered in the course of responding to the request and the matter has now been handed to the State Services Commission.
An MPI spokesperson said RNZ's original OIA request will be responded to in a fortnight, close to three months after the original request was lodged.
MPI was required to respond to the request within 20 working days but asked for an extension due to the amount of information it was going to have to collate.
At one stage it asked for the scope of the request to be narrowed from information covering the past eight years to that covering the past year. RNZ declined this request.
The misconduct MPI has uncovered is said to have happened several years ago.
Public scrutiny needed - PSA
Meanwhile, the public sector union, the PSA, said it is following any developments out of the expanded inquiry into public sector use of the firm.
The PSA said it was important there was public scrutiny of the actions of government agencies, given the publicity around this company and its activities.
It said trust in the public services was incredibly important, and anything that could shed light on concerns about the security firm would be good.