A disk drive with a write condition detector generates a write condition signal from a reference signal to warn of a high fly write or a low fly write. The reference signal is generated by the disk drive read/write head by reading a reference segment. The write condition detector processes fly-height varying components from the reference signal. The write condition detector generates a write condition signal, responsive to the fly-height varying components and the threshold, that indicates that the writing of data in a user data segment during the write operation is unsafe when the head deviates from its operating flying-height. The threshold is computed using zone coefficients determined during an intelligent burn in of the disk drive, and is based on a nominal fly height. The write condition signal is processed by a microprocessor that instructs a disk controller to deactivate a write gate controlling the write operation. The disk drive then implements verification, diagnostics and recovery steps to complete the write operation.