Thank you Shivdeep.

In WSO2 API Manager, the secret-conf.properties file will be generated at <PRODUCT_HOME>/repository/conf/security directory, only after executing the cipher tool script. But for other products e.g. WSO2 IS, this is available OOTB. Refer [1] for more info regarding cipher tool

[1] https://docs.wso2.com/display/ADMIN44x/Encrypting+Passwords+with+Cipher+Tool