The decision by Communities Secretary Greg Clark was met with "astonishment" by the council despite recommendations from a Planning Inspector that the project should go ahead.
The local authority approved proposals for the Ravenswood scheme in November 2014.
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However, the plans were called in for review by the Government in January the following year.
The application contained proposals to build 68 houses for 'affordable' rent, 24 homes for shared ownership and two specialist homes for social rent.
Council Leader David Ellesmere said the decision is likely to "cost the council millions of pounds in lost rent, grants and increased construction costs".
"All the while, Ipswich families have been left languishing on the housing waiting list and jobs in the construction industry have gone unfilled," he said.
"I cannot think of another case in the country where a planning application has been turned down because the housing wasn’t expensive enough."
(LM/MH)
