The contract description originally said Getlink, previously called Eurotunnel, was "highly likely" to go through litigation.
It said the government could be forced to pay "significant damages" if the firm was successful.
The Department for Transport says it routinely seeks legal advice.
A DfT spokeswoman said. "This multiannual contract is to provide advice on a wide range of areas relating to the Channel Tunnel and EU exit."
Elsewhere on Monday, the government announced that lorries will be able to drive straight off ferries and Channel Tunnel trains without making customs declarations in the event of a no-deal Brexit.
'Protect their business'
The government website detailing the contract with law firm Slaughter and May originally stated that Getlink had "expressed concern that their business may be disturbed or interfered with... and that this will in turn hit their profits".
It continued: "It is highly likely that they would seek to protect their business and profits through litigation against the department."
The contract description was subsequently changed to say simply that it is to provide "advice and assistance to DfT on the Cross Channel Rail Services".
Last December, it emerged that the government had awarded contracts worth £107m to three companies to provide extra ferry services in the event of a no-deal Brexit.
A BBC investigation found that Seaborne Freight, which won a contract for £13.8m to run ferries from Ramsgate to Ostend, had no ships.
In January, Eurotunnel wrote to Transport Secretary Chris Grayling to complain that they had not been considered when the contracts were awarded.
The company also warned that their award of these contracts could be illegal.
Eurotunnel has previously voiced concerns more broadly about the potential impact of a no-deal Brexit on their business.
Slaughter and May declined to comment.
Seaborne Freight said its services were due to commence in March and they expect to be ready "very close to schedule".
The government plans to pay a law firm £800,000 for advice in case Eurotunnel decides to sue over the effects of Brexit on its business.