Managing hygiene of key pairs between certificate authorities using FHE

A non-transitory computer-readable medium comprising instructions that, when executed, cause one or more processors to perform steps of:

• receiving a certificate signing request (CSR) from an entity at a certificate authority (CA);
• determining a public key of the entity from the CSR;
• applying fully homomorphic encryption (FHE) specifically to the public key to generate an encrypted query that preserves anonymity of the public key;
• querying a Certificate Transparency (CT) log in a database updated by a plurality of different certificate authorities using the encrypted query to determine whether the public key has been previously used by any of the different certificate authorities;
• responsive to the public key not having been previously used, issuing a certificate to the entity based on the public key and the CSR;
• and
• responsive to the public key having been previously used, alerting the entity to resubmit the CSR with a public key that has not been previously used.