I was in similar situation too.
Hence i submitted my Express Entry application without Japan PCC, however I added one LOE asking CIC to advise on next course of action.
When they started reviewing my application, they send me ADR (additional document request) and asked me to open the document and upload the scan copy.... They gave me separate link to upload the document (post submission)
Hope this helps !!!
All the best.
Enclosed is what i got in the ADR email
This is in reference to your application for permanent residence in Canada. In order for us to continue the review of your application, we require the following documents:
Police Certificate: You have provided proof that you applied for your JAPAN Police Certificate. To avoid further delays in processing of your application, please upload the document to your MyCIC account upon receipt.
Please upload these documents to your MyCIC account.
Please note: The above information/documents must be received within 60 days from the date of this correspondence. If this deadline is not met, your application will be assessed based on the information that was provided with your application and your application could be refused.
If the documents are not already in English or French, all documents must be accompanied by English or French translations by certified translators. When original documents are requested, you must upload the original documents to MyCIC. We do not accept copies signed by notaries.
For more information on permanent residence in Canada, please visit our web site at:
http://www.cic.gc.ca/english/immigrate/apply.asp.
Thank you for the interest you have shown in Canada.