Section 4 of the Factories Act 1948 has provision for empowering the State Government (read as Chief Inspector of Factories) to declare different departments to be separate factories. You will have to move an application for the purpose and also submit Factories License form separately for the hazardous process factory and another for the remaining factories.
Splitting of factories has certain advantages and also disadvantages. You need specified Factory Occupier and Factory Manager, submit all forms and maintain registers separately, pay license fee individually. Labour department can harass for separate compliance regarding canteen, ambulance, creche, Welfare Officer, Safety Officer, Certifying Surgeon etc From my experience of dealing with this matter, it is felt that over a period of time this becomes cumbersome. So weigh the pros and cons thoroughly before taking the decision as splitting up is a one way process and reversing it is a herculean task although legal provision exists for it too.