I am a spouse of EU national and want to apply for Schengen visa as a family member of EU citizen.Can I send my visa application and documents to Netherlands Embassy in Malaysia while I am a citizen of Pakistan and also currently living in Pakistan.
Probably not. A Schengen consulate is only supposed to accept visa applications from people who reside in the consulate's jurisdiction. There is an exception, but it seems that in practice the threshold for invoking this exception is very high.
Article 6 of the Schengen Visa Code:
Consular territorial competence
An application shall be examined and decided on by the consulate of the competent Member State in whose jurisdiction the applicant legally resides.
A consulate of the competent Member State shall examine and decide on an application lodged by a third-country national legally present but not residing in its jurisdiction, if the applicant has provided justification for lodging the application at that consulate.
As a resident of Pakistan, therefore, to apply in Malaysia you must be in Malaysia and you must have a good reason for not applying in Pakistan.
Examples of "good reasons" may be found in section 2.8 of the Handbook for the Processing of Visa Applications (pdf). The examples imply that the reason should be something like (1) a planned absence during the three-month period allowed for an application or (2) an unforeseen urgent circumstance. Anecdotal evidence suggests, however, that at least some consulates refuse to consider applications from nonresidents altogether.
Furthermore, you are probably aware of the following points, but they should be noted as well. First, whether you can apply for the visa at a consular post of the Netherlands depends on where you plan to travel. Second, to qualify for a visa as a family member of an EU citizen, you must be either traveling with or joining the EU citizen family member.