You must contact Malaysian Immigration to inquire about extending the stay. This is a circumstance beyond your control, they should be able to help you when extending your stay. The Embassy of Indonesia has limits to involvement in host country visa policies. If you are looking to return home, the Embassy of Indonesia can assist you in the form of an evacuation flight (unlikely in this scenario) or the like.
If you just want to extend the stay, assuming you are in KL, here are 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
You can find other contact details on the following websites.
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