Under NEC 3 can a Contractor respond to an Early Warning Notification by rejecting it?
In short - no, or at least that is my practical response. What is there for either Party to reject? Why would they need to be so defensive?? The Project manager here (assuming this is ECC) has raised an issue that they believe to be a potential problem and you should respond accordingly. This could be as a written response or even better would be for the matter to be discussed at a risk reduction meeting and the actions to be taken to avoid or reduce the risk recorded onto the Risk Register.
Too many people think of the early warning process as being attached to cost and that should not be the case. The answer to your question is to respond by making it clear why the issues raised are not going top be an issue.
Would like to reinforce Glenn’s response by saying that the entire purpose of Early warnings is to avoid, mitigate or reduce potential risks. Issuing an early warning is a positive pro-active action. Much can be lost in translation in written communications and that is why it is good to discuss early warnings in a risk reduction meeting face to face to understand the risk.