More civil servants intended to lodge complaints against Dominic Raab over his behaviour but allegedly pulled out for fear of being identified.
Senior lawyer Adam Tolley KC is investigating a number of complaints about the deputy PM's behaviour.
But the BBC understands a number of civil servants who had intended to lodge formal complaints did not.
, who was reappointed by Rishi Sunak as a cabinet minister, has denied allegations of bullying.
The MP for Esher and Walton previously served as justice secretary and deputy prime minister under Boris Johnson
A close ally of Mr Sunak, Mr Raab
was sacked from those roles when Liz Truss became prime minister in September.
was reappointed as both justice secretary and deputy prime minister, after Mr Sunak became PM.
He is facing multiple complaints from his first stint at the Ministry of Justice (MoJ), and his time as Brexit secretary in 2018. He is the subject of a single complaint from his tenure as foreign secretary.
The BBC has found that other civil servants who allegedly planned to file complaints did not. This decision came after they were told they would have been identified to Mr Raab
as part of the investigation by Mr Tolley.
It is understood this is standard practice for an investigation not to take testimony from anonymous sources.
It is suggested some feared being identified in case Mr Raab
were to remain in post, and he would know they had complained against him.
The prime minister will decide the justice secretary's political future when Mr Tolley concludes his investigation.
The BBC understands some staff who have not directly complained are now offering to act as witnesses to the inquiry. Mr Tolley has been conducting interviews about Mr Raab
's alleged conduct since the start of the year.
Whitehall sources say that Mr Raab
has modified his alleged behaviour on his return to the MoJ last autumn.
The senior civil servants' union, the FDA, wants to see the complaints process overhauled.
Confidence in the system was all but destroyed after former home secretary Priti Patel
remained in post after she was investigated for bullying, the union has claimed. The FDA believes this had led to a reluctance by some of their members to make complaints.
The government has promised that Mr Tolley "will have access to all the information he wishes to see" and that his report on Mr Raab
's conduct will be made public.
When the inquiry was announced last November, Mr Raab
said he would "thoroughly rebut and refute" the claims against him in a "fair and formal" setting.
He said he was "confident" he had behaved "professionally throughout".