"There are 93 agencies who are currently customers of FXNZ through the all-of-government contracts, who have been notified of this outcome," he said.
Fuji Xerox had accepted a voluntary suspension in July on those two contracts plus a third deal providing print devices and print device management services and was extended until October to allow for more talks between MBIE and the company.
In June, Japanese parent Fujifilm Holdings revealed $355 million of "inappropriate accounting" in operations in New Zealand and Australia between 2011 and 2016, according to a report by an independent investigation committee.
Thomas said MBIE gave the company clarity on what is required for the company to meet requirements for the suspension to be lifted.
"We remain committed to working with Government and to regaining and rebuilding trust with all of our stakeholders.
"We are taking this seriously and are committed to rebuilding our trust and long term relationship with Government."
Last week, Fuji Xerox appointed Thomas, former MBIE deputy chief executive of corporate services, as its new managing director, having hired him last year as chief operating officer.
MBIE said it won't comment further on the Fuji Xerox contracts.