Oyston Estates cried foul after its land at Lytham Moss, Lytham St Anne's, was excluded from sites viewed as part of the existing settlement under the St Anne's-on-Sea Neighbourhood Plan.
Mr Justice Kerr found that the company had "arguable" grounds for complaint, but went on to dismiss its challenge. He said Oyston Estates had left it too late to challenge that part of the neighbourhood plan to which it objected.
The plan was adopted by Fylde Borough Council in May, following a local referendum. The judge said the whole process would be put "under a cloud" if Oyston Estates' challenge was allowed to go ahead.
The company's land is part of a biological heritage site and is close to a habitat for wintering birds. But here is an existing housing estate on one side of it and, on the other, planning permission has been granted for 1,150 homes.
An independent examiner who looked into the proposed neighbourhood plan recommended that Oyston Estates' land should be included within the settlement boundary. But in March the couincil rejected the examiner's views, deciding that the site fell outside the town limits.
The neighbourhood plan was adopted on May 26 following a local referendum.
Mr Justice Kerr said Oyston Estates challenge to the council's "merited full consideration" but noted that it had not lodged its legal challenge until July, well after the six-week period allowed for in planning law had expired.
The court had no power to extend the deadline and the council's decision was therefore "no longer susceptible to challenge", the judge ruled. Recognising the importance of the issue, however, he granted Oyston Estates permission to challenge his ruling in the Court of Appeal.
R (Oyston Estates) v Fylde Borough Council. Case Number: CO/3187/2017
This article was updated on 6/12/17 to remove incorrect information on the neighbourhood plan poll result.