Research by charities Crisis and the Joseph Rowntree Foundation suggested "informal" methods used by councils to tackle the problem had masked a 9% rise in cases in 2013-14 - to 280,000 cases.
Official statistics put the number of "accepted homeless" cases at about 52,000 last year, down 3% from 2012-13.
The government said the charities' figures were "misleading".
The annual independent study - which drew on a survey of England's 326 councils in 2014 - said the rise in the number of people facing homelessness was in part the result of benefit cuts and sanctions.