The Covid inquiry is conducting four weeks of hearings looking at deals to buy £15bn of PPE during Covid.
The National Crime Agency (NCA) has been investigating PPE Medpro since May 2021 over suspected criminal offences committed in the procurement process.
To date no charges have been brought and the Crown Prosecution Service has not been instructed in the case. Baroness Mone, 52, and Mr Barrowman, 59, have both denied wrongdoing.
A special inquiry hearing about the company will take place behind closed doors next week after Baroness Hallett said she was satisfied there was a risk of prejudice to the ongoing NCA investigation if "sensitive evidence" was made public.
In a joint statement, Baroness Mone and her husband said the decision to hear evidence in private was "a blatant betrayal of transparency and justice" and accused the NCA of waging "a ruthless campaign" against them.
The couple said: "While the inquiry refused to exclude PPE Medpro, it handed the NCA the power to dictate the proceedings behind a wall of secrecy, ensuring that only their version of events is heard – while we are denied the right to defend ourselves."
In a social media post, Baroness Mone said she did not realise that the company would be "specifically profiled" by the inquiry until the end of February.
"Until then, it was understood that discussions were general, covering overall PPE procurement, not targeting any individual entity," she added.
The couple's statement was released after their second approach to be made core participants was rejected.
Baroness Hallett said allowing the application to proceed would have led to a "further diversion of resources" and have caused "significant disruption" to the inquiry's timetable.