I’m holding malaysia passport

Kenny, do you mean the entry permit for Macau or Mainland? If for mainland, you can't get it upon arrival. If for Macau, actually you don't need it in case that your planned visit is not longer than 30 days.

if i want to apply the mainland entry permit, where should i submit the document and take how long to process (macau)

You had better not apply from Macau if you don't have residency there because there is a risk that you will be refused. Anyway, if you apply from there, you should submit the documents to the Office of the Commissioner of PRC Foreign Affairs Ministry. The whole process for approval takes four working days.