Water pollution, especially by oil, organochlorines and heavy metals associated with agricultural run-off and logging activities, poses a serious threat to the flat-headed cat through contamination of its prey. This is a major problem throughout much of the flat- headed cat's range. In addition, waterways are often the areas first cleared by people as settlement expands into the forested areas.
The flat-headed cat is seldom encountered and is believed to be rare.
Prionailurus planiceps is considered as "Vulnerable" by the IUCN. CITES lists the species as "Appendix 1".