One of the train carriages had been modified into a hearse with wide doors and a rotating table to carry the coffin.
However, plans to send the train to Scotland were scrapped amid fears that the route would be disrupted by crowds of trespassers and protesters, The Telegraph reported.
The paper said a palace source said the decision, made to ensure safety and security, had been taken on the advice of numerous organisations, including police, government departments and local councils. It is understood it would have caused disruption to public rail timetables.
The Queen will now be flown by RAF C17 from Edinburgh to London. A palace source told the Telegraph that the use of the RAF plane had been the original plan, to which they have now reverted.
The aircraft will leave at 6pm bound for RAF Northolt before the coffin goes on to Buckingham Palace.
Nigel Harris, editor of Rail magazine, called the palace’s decision to use the aircraft "wrong-headed".
He told the paper: "People have been denied their chance to pay their respects to the Queen. I don’t think she would have gone along with that."
He added: "Deciding not to use the royal train to take Queen Elizabeth II back home to London on her last journey was, in my view, a major blunder by government, Palace and railway. Millions - and I do mean millions - of folk living south of the Scottish border and north of London have been denied that powerful, humble experience."
The coffin will be accompanied on the journey by the Princess Royal.
It comes as motorists have been warned of extensive, additional closures and diversions in Edinburgh on Tuesday as the Queen’s coffin is taken from St Giles’ Cathedral on the Royal Mile to the airport.
The cortege will depart Scotland in the afternoon and a number of roads will be closed to traffic between 4pm and 6.30pm.
The city council warned the arrangement will have a “significant impact on public transport services across the city and surrounding trunk roads”, including the M8 and the City Bypass.
While the airport stays open, the airspace around it will close temporarily this afternoon to ensure the smooth take off of the RAF plane taking Her Majesty’s coffin south.
The main roads affected by the additional closures are Johnstone Terrace, Lothian Road, Queensferry Street, Dean Bridge and Queensferry Road.