Newport council rejected plans to split the existing Duffryn High School site and create a new facility alongside it.
The school would have benefitted from a new building, but now has "virtually nothing", said head teacher Jon Wilson.
Newport's chief education officer James Harris said there were still plans for "substantial investment".
But he said the money would be used in a different way after the Welsh medium school proposal was rejected.
Mr Wilson said the school had been promised new buildings "time and time again" and called the situation "a mess".
After the proposal was rejected because of flooding fears, the council said it would begin searching for an alternative location for a Welsh-medium school.
Rejected plans to build a Welsh language secondary school in Newport have been called "a mess" by the head teacher who was due to share the site.