In October 1601, the Society of Jesus distributed to the provincials a cipher to replace a previous one for use in communication with the General resident in Rome (letter found in Peru from the General to padre Rodrigo de Cabredo, the provincial of Peru). (The Jesuits are organized into provinces, each having a provincial superior or simply "provincial". The head of the order is the general superior or the General. (Wikipedia))
This is a simple polyalphabetic cipher consisting of six rows of cipher alphabets, each having a regular alphabetical sequence (without J, K, V, Y) with different starting positions. Enciphering is begun by looking for the first letter to be enciphered in the first row and taking the number above the letter as the cipher for the letter. The second letter is enciphered with the second row, and so on. To encipher the seventh letter, the first row is used again.
Punctual switching of the six rows is essential in correct enciphering. If a row is repeated or skipped, the resultant cipher would be undecipherable. See another article, which describes John Adams' troubles with polyalphabetic ciphers of James Lovell.
Secret writing was in use even from the earliest years of the establishment of the Jesuits in Peru. A letter of P. Juan de Zuniga to the General, Francis Borgia, dated Lima, 31 December 1572, used code words. In 1573, Juan de la Plaza, newly appointed visitor ("visitador" or inspector) of the Province of Peru carried with him a cipher key.
A brief description of the Jesuit intelligence system is found in Robertson, William, The history of the reign of the Emperor Charles the Fifth Vol. 2 (1895) p.322 (Internet Archive), according to which each of the provincials or rectors had a particular cipher from the General.
Guillermo Lohmann Villena (1954), 'Cifras y Claves Indianas,' Anuario de Estudios Americanos, XI, p.285 (esp. p.321-323)