Transport minister Stephen Byers said contractors could make up part of the 40-strong membership of the replacement organisation, and would act like shareholders.
The not-for-profit company proposed by Byers would have a board of 12 and 15 directors, with other places taken by the Strategic Rail Authority, passenger groups and train operating companies.
Skanska Construction Group chief executive Keith Clarke said the new body did not need to have representatives from the supply chain.
He said: "They [contractors and consultants] do not need to be part of that public service body. They have different interests – they need to make money for their shareholders. There is a huge conflict of interest."
EC Harris chairman Richard Clare said: "The government is going to have to be very careful about conflicting interests. There would be huge commercial issues if there is representation from the industry."
Contractors need to make money for their shareholders. There is a huge conflict of interest
Keith Clarke, chief executive, Skanska Construction Group
Clare also voiced concern about the management structure of the replacement body, warning that the involvement of 40 "stakeholders" could prevent quick decision-making.
Clare added that Railtrack's collapse at the start of the month was already impacting on major projects such as the West Coast Main Line. Tony Fletcher, general manager of the scheme, resigned last week to join consultant WS Atkins.
Clare said: "We are very concerned about the integrity of major projects. We must not lose focus on these schemes."
Railtrack's administrator Ernst & Young said it was undertaking a full-scale review of Railtrack's operations, including the West Coast Main Line. Results of the review would not come out until the end of the year, a spokesperson said.