Here is one relevant passage in Suetonius, Divus Iulius, 56.6, describing the Caesar cipher:

Epistulae quoque eius ad senatum extant, quas primum uidetur ad paginas et formam memorialis libelli conuertisse, cum antea consules et duces non nisi transuersa charta scriptas mitterent. Extant et ad Ciceronem, item ad familiares domesticis de rebus, in quibus, si qua occultius perferenda erant, per notas scripsit, id est sic structo litterarum ordine, ut nullum uerbum effici posset: quae si qui inuestigare et persequi uelit, quartam elementorum litteram, id est D pro A et perinde reliquas commutet.

There are extant likewise some letters from him to Cicero, and others to his friends, concerning his domestic affairs; in which, if there was occasion for secrecy, he wrote in cyphers; that is, he used the alphabet in such a manner, that not a single word could be made out. The way to decipher those epistles was to substitute the fourth for the first letter, as D for A, and so for the other letters respectively.
(translation by Alexander Thomson, 1889)

See Perseus for more context.

The bit I highlighted gives one answer to your question: per notas scribere.

Here is one relevant passage in Suetonius, Divus Iulius, 56.6, describing the Caesar cipher:

Extant et ad Ciceronem, item ad familiares domesticis de rebus, in quibus, si qua occultius perferenda erant, **per notas scripsit**, id est sic structo litterarum ordine, ut nullum uerbum effici posset: quae si qui inuestigare et persequi uelit, quartam elementorum litteram, id est D pro A et perinde reliquas commutet.

There are extant likewise some letters from him to Cicero, and others to his friends, concerning his domestic affairs; in which, if there was occasion for secrecy, he wrote in cyphers; that is, he used the alphabet in such a manner, that not a single word could be made out. The way to decipher those epistles was to substitute the fourth for the first letter, as D for A, and so for the other letters respectively.
(translation by Alexander Thomson, 1889)

See Perseus for more context.

The bit I highlighted gives one answer to your question: per notas scribere.