An independent Planning Inspector recommended that proposals for 94 affordable homes at Ravenswood should go ahead.
The plans were called in by the Government and have now been rejected by the Secretary of State for Communities & Local Government.
The planning application was to build 68 houses for affordable rent, 24 homes for shared ownership and two specialist homes for social rent.
The government ruling raised concerns that the affordable homes were “not truly integrated into market housing”.
Council Leader David Ellesmere said: “The Secretary of State has now blocked the application on the grounds that the development should contain more homes for sale.
“This is an astonishing decision.
“I cannot think of another case in the country where a planning application has been turned down because the housing wasn’t expensive enough.
“The length of time it has taken the Government to take this 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.”
The Council said it will now consider the Government’s decision before it considers its next steps.