John Saunders, who runs a garden centre and is curator of the Stondon Transport Museum, has been told by Mid-Bedfordshire DC that the replica 18th century sailing vessel may have to go.
But Mr Justice Ognall said yesterday that Mr Saunders' legal challenge was premature as the council had not yet taken any active steps to enforce the replica's removal.
If the council now serves an enforcement notice, Mr Saunders may go back to court.
His solicitor, Douglas Raine, said outside court that the ship's exterior was complete, but Mr Saunders was reluctant to start work on the interior while his legal position remained unclear.
The council in January this year said it intended to take steps to enforce the removal of the replica ship which it claims was erected in breach of planning control.
Mr Raine commented: 'Mr Saunders is now in limbo, unable to go forward because there is nothing that he can challenge. What we were trying to do was bring matters to a head so that he can get on with his project.
'This is just the beginning in the sense that we must now wait for the enforcement notice.'
Outside the transport museum, alongside the ship, stands a collection of classic cars, a vintage fire engine and old military vehicles, said Mr Raine.
'He designed the exhibit from the naval architect's drawing of the 'Endeavour'. He took from the architect's drawings the necessary engineering details and took what was needed to manufacture the replica. He has virtually re-built the 'Endeavour' from the original naval architect's drawings. It will be a phenomenal attraction; it's a tragedy that it is not finished and available for the public to see.'
Mr Saunders claims the replica ship did not need planning permission as it is not a fixed structure.
Mr Justice Ognall refused to grant leave for Mr Saunders to mount a judicial review challenge, but said he could return to court 'in the event that the council serve an enforcement notice'.