The committee slammed the DCLG's handling of the housing and regeneration programme: "Management of the programme has been weak and not demonstrably added value to it."
The Thames Gateway would sit with other housing growth programmes at the Homes and Communities Agency and benefit from its housing and regeneration expertise, the report argues.
The DCLG would then be better placed to concentrate on policy development and achieving cross-government co-ordination, it adds. Committee chairman Edward Leigh claimed that the gateway just amounts to "a group of disjointed projects".
A DCLG spokeswoman said: "It is baffling that the report should propose handing the gateway to an agency that will not exist for two years. The pace of change there means that the report is already out of date."
The department will publish its delivery plan for the sub-region at this month's Thames Gateway Forum, setting out costed plans for 160,000 homes in the area.
Campaign to Protect Rural England Thames Gateway project leader Nigel Kersey said: "The real issue is how upfront investment can be obtained to fund public services in growth areas."
The Thames Gateway: Laying the Foundations is available at PlanningResource.co.uk/doc.