UPDATE: Flights are operating to Indonesia that allows you to fly out, at a very reasonable price. The below advice still applies if your host country ceased flights, like India, or your country of citizenship ceased flights (again India).
You have to contact Malaysian Immigration to know about the stay extension. This is a circumstance beyond your control, they should be able to help you on extension of your stay. Indonesian embassy have limitations on involving in visa policies of host country. If you are looking to go home, Indonesian embassy may help in form of an evacuation flight (unlikely in this scenario) or similar.
If you just want to extend the stay, Assuming you are in KL, this is the contact details.
Jabatan Imigresen Wilayah Persekutuan Kuala Lumpur,Aras LG, 1,2 & 5,
Kompleks Kementerian Dalam Negeri (KDN), No 69, Jalan Sri Hartamas 1,
Off Jalan Duta, 50550, Kuala Lumpur
Further contact details can be found in the following websites.