Unfortunately, urine cytology tests are not 100% accurate. This is why they are used more as indicators that something more needs to be checked out than as a means of diagnosis. Most often they are erroneous in the other direction, suggesting that malignancy is present when it is not. Your doctor was absolutely right in going ahead with cystoscopy no matter what the urine tests said.
Diagnosis 2-08 Small papillary TCC; CIS
BCG; BCG maintenance
Vice-President, American Bladder Cancer Society