Passport loss/ Visa transfer

Hello,
I'm currently living in Japan under a student visa for two years.
However, I lost my passport recently. I'm currently making a new one, but this new passport will not have the visa stamp on it.

I contacted the immigration office, and they told me that they could only transfer the landing stamp, and that Visa are not being transferred anymore since the new immigration system.

My question is : I want to go back to my country for three weeks in August. Will I be able to come back to Japan if I do not have the Visa stamp on my passport? I have my resident card with the duration and type of Visa written on it, but I do not know if it's enough.

Thanks!

Have your school contact immigration immediately to confirm this as well as what you need to do upon your return. Your tuition money is their incentive.