The Department for Culture, Media and Sport is understood to have sent a letter to English Heritage at the end of last month stating that it intended to list part of the 4.2 ha Bishopsgate Goods Yard.
Later the same day, a departmental official is believed to have telephoned an EH inspector, saying that the letter should be ignored as the matter was still under review.
EH, along with local community groups and the Prince's Foundation, called on the department to give ancient monument status to the historical Braithwaite Viaduct and list the rest of the site. The alliance feared that the site would be demolished to make way for the proposed extension to the East London Underground Line, and a swath of commercial development.
The Corporation of London countered that listing the site would delay the construction of the line. Michael Oliver, the Lord Mayor of London, met with the Prince of Wales to tell him that the listing would mean the extension may not go ahead as it would have to be built above the Braithwaite Viaduct and its adjoining arches.
A source who has seen the letter said the department had decided that Braithwaite Viaduct should be given a grade II listing, but that the arches should not be listed.
Grade II listing is less restrictive to development than ancient monument status, but would still mean that demolition was unlikely. The source added: "This [the retraction of the letter] is a unique occurrence."
It is unclear why the DCMS withdrew the letter, but a spokesperson for the department said earlier this month that a decision on the listing had been delayed because of political pressure.
An observer of the saga at Bishopsgate said: "The department is caught between a rock and a hard place. Inevitably this is a political decision."
The DCMS declined to comment.
EH regeneration adviser Martin O'Rourke would not confirm the existence of the letter, but said EH was still awaiting a decision from the department.
A decision is unlikely to be made until next week at the earliest, as secretary of state Tessa Jowell is abroad this week.