Deputy prime minister John Prescott turned down schemes in Felsted, Essex, in Fareham, Hampshire and in Solihull, in the West Midlands. Together, they would have created 1109 homes.
In July, Prescott called for 39,000 new homes a year in the South-east alone and at the urban summit two weeks ago he criticised housebuilders' development records.
The schemes were rejected for failing to meet the government's PPG3 planning guidance.
Enodis Property Developments' 655-home Felsted scheme was refused for not including 25% affordable housing – the amount suggested in the area's housing needs study. However, Prescott did praise the scheme for its high density of 31 dwellings a hectare, and a housing inspector report recommended approval.
Laing Homes' 288-home scheme in Fareham was rejected as it was proposed for greenfield land. Under the "plan, monitor and manage" rule in PPG3, councils are advised to build on brownfield land. But the site was recommended for housing under the council's local plan, and again Prescott praised the density of 36.5 dwellings per hectare.
Wimpey Homes' 166-home development in Solihull was rejected after a housing needs survey suggested that a high level of affordable housing was necessary in all developments in the area. The local council did not demand affordable housing from Wimpey and argued that there were enough such homes on nearby developments.
Roger Humber, a former House Builders Federation chief executive, said that government policy was making the housing shortage worse. He said: "The government is hair-splitting. It has lost the wood for the trees."
A spokesperson for the Office of the Deputy Prime Minister defended the decisions. He said: "A scheme might meet a number of our needs, but if it is lacking in a key area there is a good chance it will be rejected."