She needs to contact the Philippine Embassy there for help. Here is how to contact them.

Embassy of the Republic of the Philippines  
Address: 1, Changkat Kia Peng, 50450 Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
Phone:+60 3-2148 4233

Normally we don't say a person "ran away" from their employer unless they are afraid for some reason and normally there is some sort of illegal activity. If this is the case your friend should contact the Filipino embassy in Malaysia.

Normally at a job we resign or quit...running away is what is usually associated with stuff like running from a slave owner or criminal boss.

get back her passport first if she didn't escape with it or alternatively go to the Philippine embassy in Malaysia for help

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