Whitehall documents obtained by the Guardian under freedom of information legislation show that in January 2013, Wilkinson declared he was a director of FCP and owned shares in the company.
According to the DfT, his long career in the rail industry had included work on the privatisation of British Rail and leading negotiations on both sides of franchising.
GTR said it had regularly employed the services of FCP since 2005 at an annual fee of about £18,000.
A spokeswoman said it had paid FCP more than £10,000 for general consultancy services between September and November 2013, adding “this would have been the time when we were working on our bid [for the franchise]”.
The Guardian asked Keolis when it had used FCP, but the company declined to answer, saying: “We don’t comment on the detail of any commercial relationships.”
FCP said it could not answer questions about clients because it was bound by strict confidentiality.
“Our work is wide ranging and we have always maintained comprehensive confidentiality and conflict of interest processes with all our clients, in line with public procurement rules,” a spokesman said.
Wilkinson he made to a public meeting in south London organised by a Conservative MP to discuss the railways in February last year.
: “Over the next three years, we’re going to be having punch-ups and we will see industrial action, and I want your support.”
“I’m furious about it and it has got to change – we have got to break them.
“They have all borrowed money to buy cars and got credit cards,” he said.
“They can’t afford to spend too long on strike and I will push them into that place.
“They will have to decide if they want to give a good service or get the hell out of my industry.”
Rob Evans and Lucas Amin add:
The Labour party has called for an investigation into disclosures that the civil servant who awarded its rail franchise did so while owning a large share in a consultancy that had been advising the troubled operator’s parent company.
Andy McDonald, the shadow transport secretary, said the “expose the murky world of rail franchising” and pressed for an investigation by the head of the civil service.
“It is clear that the relationship between the Department for , private companies who profit from our railways, and lobbying and consultancy firms is uncomfortably close,” he said.
McDonald’s call for an investigation centres on Peter Wilkinson, who had been hired by the Department for Transport (DfT) to be its franchising director.
Wilkinson was involved in awarding the in May 2014.
For 20 months after he was recruited to the department, he was a director and the joint main shareholder of First Class Partnerships (FCP), a transport consultancy he had been managing since 2002. He was employed by the DfT as a contractor under an agreement with FCP.
Govia had been a longstanding client of First Class Partnerships and had been paying it for advice six months before the franchise was awarded.
Whitehall documents show the DfT eventually concluded that Wilkinson had a clear conflict of interest between his shares in FCP and his government work as the arrangement in which he had been seconded from FCP “feels very uncomfortable”.
On Tuesday, McDonald said:
“For complete transparency it is essential that the secretary of state [for transport] refers these allegations to the head of the civil service so they can be investigated.
“Without a full and open investigation that addresses these alleged conflicts of interest in the awarding of the GTR franchise and other franchises, suspicions will remain about how these rail contracts are awarded.
“Passengers, taxpayers and stakeholders need answers if they are to have any confidence in our railways and how they are being run.”
Referring to Wilkinson, Louise Ellman, the Labour chair of , said:
“There are unanswered questions about his role at the department.”
The DfT has said while Wilkinson worked as its interim franchising director between January 2013 and October 2014, there were strict procedures to prevent conflicts of interest, while FCP implemented measures to ensure that any conflicts of interest were avoided.
In a statement, a DfT spokesperson said:
“The department regularly contracts and recruits people with relevant industry and commercial expertise, to help it achieve the best result for passengers and taxpayers.
“We have robust safeguards to guard against any conflicts of interest.
“Decisions on franchise awards are taken by the department following a fair and open competition.
“Each franchise award is subject to thorough and independent audit.”
Since November 2014, Wilkinson has been the department’s managing director of rail passenger services on an annual salary of £265,000.
Trade unions allege he is “ , after he told a public meeting that he and others wanted to “break” train drivers.