ISS is the biggest project ever undertaken in space
It was reacting to the US space agency's (Nasa) Advisory Council endorsement of the idea.
But Esa accuses the council of failing to take on board the interests of European partners. If the cuts go ahead, Esa says, the US-European partnership will be profoundly affected.
The council's views are not binding on Nasa executives, but as the standing body of experts set up to offer guidance to the space agency, its opinions carry great weight.
Partnership threatened
Esa said it did not agree with the council's position.
The advisory council is of the view that the ISS should carry no more than three residents at any one time.
The European agency argued that a permanent three-person crew would not provide for "a viable space station for world class research".
This, it believes, would severely limit the participation of European astronauts on the orbiting platform.
Esa urged Nasa's Advisory Council "to reject or amend those recommendations which, if implemented, would jeopardise the partnership, invalidate the ISS as a facility for world-class research in space and undermine future US-European cooperation".
Nasa has said it will make no formal comment on the council's findings until senior agency management have had an opportunity to do a comprehensive assessment of the recommendations.
Uncompromising criticism
The advisory council issued its report after studying the results of the International Space Station Management and Cost Evaluation (IMCE) Task Force.
The IMCE was asked to perform an independent external review of the space station programme.
The panel was uncompromising in its criticism of what it said were serious flaws in the agency's management.
"The existing deficiencies in management structure, institutional culture, cost estimating and programme control must be acknowledged and corrected for the programme to move forward in a credible fashion," it said.
The independent task force looked at ways the ISS project might be scaled down to reduce costs.
It suggested lowering the number of people working on the station, reducing the number of shuttle flights to the platform, and reorganising the station management.