V/Line hired a general manager and paid him more than double his predecessor's salary, despite him refusing to provide a resume to the company's human resources department or submit to a probity check, Victoria's anti-corruption commission has been told.

Key points: Manager actively recruited for role by former colleagues, IBAC told

Manager actively recruited for role by former colleagues, IBAC told Role was not advertised or put to tender, counsel assisting the inquiry says

Role was not advertised or put to tender, counsel assisting the inquiry says Salary for the role was set at $414,000 per year

The Independent Broad-based Anti-corruption Commission (IBAC) was told Alan Clifford, who was appointed general manager of rolling stock engineering at V/Line in 2014, allegedly got angry and threatened to resign when he was pressured to provide the documents.

A witness told IBAC then-head of V/Line, Theo Taifalos, directed her to stop pursuing the documents - a move the witness described as an "unusual directive".

Mr Taifalos and David Cameron, who was executive general manager of asset management, actively recruited Mr Clifford to V/Line, first as a consultant, then as a manager about a month later, IBAC heard.

All three men had worked together at Sydney Trains.

Mr Clifford's role was not vacant at the time he was approached, but the incumbent was terminated around the time Mr Clifford was offered the job.

The role is a specialised position that included managing the fleet and safety.

Contrary to V/Line's recruitment policies, the position was not advertised or put to tender and no other candidate was considered, according to counsel assisting the inquiry, Ian Hill QC.

Mr Clifford's salary was set at $414,000 a year, and more than double his predecessor's pay, Mr Hill said, and more than Mr Taifalos received as chief executive.

Witness says HR told 'not to pursue it'

Witness Elaine Seckold said V/Line's human resources department chased Mr Clifford for months to provide routine information to prove he had the correct engineering qualifications for his position, and had passed probity checks.

But she said he appeared reluctant to do so and told her the documents were "in the too-difficult box".

He allegedly added that he was "cheesed off" and threatened to resign if human resources kept asking for the information.

Former V/Line chief executive Theo Taifalos has denied any wrongdoing. ( ABC News )

Two witnesses said Mr Clifford said he was not going to cooperate as it "wasn't part of the deal" between himself and Mr Taifalos.

Ms Seckold said soon after, Mr Taifalos began shouting, demanding to know why they were asking for documents from Mr Clifford.

She said Mr Taifalos yelled that he would vouch for Mr Clifford before any regulatory body, and told her "we were not to pursue it anymore", an instruction she said was "unusual".

Mr Taifalos has denied he had any deal with Mr Clifford, saying the company still needed proof of Mr Clifford's qualifications.

When asked why two witnesses had sworn that he was yelling and questioning why HR was asking for documents, he said they were mistaken.

Head of human resources Jennifer Kelman later wrote an email to Mr Clifford, apologising for the "misunderstanding".

"I have been advised there is no requirement for you to provide your qualifications and complete a probity [check]," she wrote.

Mr Hill said aspects of Mr Clifford's recruitment raised real concerns as to the integrity of the process adopted.