Application of Visa

Hi, I am Korean and staying in Ibaraki of Japan.
I will attend a conference in China and I also got a invitation letter from Zhejiang university.
I will stay at Hangzhou for 5 days (11/22-26).

To apply to an entry permit for me, can I visit the embassy in Tokyo and apply it by myself ?
I will prepare my passport, the application form, the invitation letter, and fee (4000 yen).
If not possible, do I need to contact with a travel agency ?
In the case, please let me know a contact number.