Applications for short-term (Schengen) visas can only be submitted through the external provider VFS Global in Jakarta and in specific cases (family members of EU citizens, humanitarian cases worthy of consideration) also at the Embassy of the Czech Republic in Jakarta.
Applications for short-term Schengen visas are submitted at the Jakarta Visa Center operated by the outsourcing company VFS Global at:

Kuningan City, 1st Floor L1 30-32, Jl. Prof. DR. Satrio No.K av. 18, RT.14/RW.4, Kuningan, Kareta Kuningan, Setiabudi, South Jakarta City, Jakarta 12940

An appointment for a short-term Schengen visa must be booked in advance in the online booking system: https://visa.vfsglobal.com/idn/en/cze/

It is to be noted that the Embassy does not administer the visa centre's appointment system and is not entitled to interfere with it in any way.

For capacity reasons and with regard to the above, the staff of the Consular Section do not respond to e-mail requests regarding the assignment of a date for submitting a visa application at the visa center. In these matters, it is necessary to contact the visa centre directly via the e-mail address info.czechid@vfshelpline.com or telephone number +62-21 - 50957960 (08:00 – 12:00 and 13:00 – 16:00 o´clock  from Monday to Friday).

Visa applications cannot be submitted at honorary consulates of the Czech Republic in Indonesia.