Epping Forest District Council refused permission for traveller Miles O’Connor to use land at Sunnyside, Carthagena Estate, Nazeing, for two gypsy pitches and also issued an enforcement notice ordering the travellers off the site.
When O’Connor challenged that decision, Eric Pickles backed the stance of the council.
Now Mr Justice Wyn Williams has overturned that ruling and ordered Pickles to reconsider the matter.
He ruled that Pickles was wrong to take the view he took over the possible flood risk at the site.
The judge said Pickles' view, which conflicted with the view of a planning inspector, did "not stand scrutiny".
Quashing the decision and ordering a rethink, he said: "The first respondent's (Pickles') decisions to dismiss the appeal against the refusal of planning permission and to uphold the enforcement notice (subject to extending the period for compliance therewith) were tainted by illegality for the reasons I have given."
O’Connor hopes ultimately to gain approval to stay on the land, where he lives with his wife Margaret and six children.
The council refused planning permission and issued the enforcement notice over what it considered an unlawful use of the land in 2012.
O’Connor appealed, but while a planning inspector who considered the case recommended scrapping the notice and issuing a temporary planning permission for four and a half years, the communities secretary disagreed.
He took the view that the inspector was wrong to conclude that the site would be safe from flood risk for the four and a half year period.
O’Connor bought the land in 2010, and, in 2011, began clearing and fencing it, and laying hardstanding. The breach of planning control alleged by the council included this and the stationing of caravans and mobile homes on the land.
R on the Application of O'Connor v Secretary of State for Communities and Local Government. Case Number: CO/632/2014