In your situation, I would start by speaking to your employer. It might be possible for you to get a work permit, if your employer is willing to sponsor you.
As your current visa is very close to expiring, it might be necessary to go back to Pakistan and apply through the local Japanese embassy. Many employers are familiar with dealing with the visa process, so they will be able to provide more information for you.
It might also be an idea to speak to an immigration lawyer to see if there is anyway you can transfer onto a work permit without having to leave the country.
Get an overview of the visa process for Japan on Visas for Japan.