All your correspondences and additional submissions should be sent to the visa office processing your application. This is what is instructed to applicants after your application has been transferred by CIO to a visa/processing office.
If it is the Embassy of Canada in Manila who is processing your application then all submissions, including payment of additional fees are sent to CEM. Please see here for payment instructions and the amount for RPRF.
http://www.canadainternational.gc.ca/philippines/visas/fees-frais.aspx?lang=eng
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Current applications: If you are paying additional fees for an application currently being processed in Manila, you will receive instructions on how to pay the fees.
Payment Instructions - Philippines
Fees must be paid by bank draft, certified cheque, postal money order (PMO) or manager's cheque. Cash payment is not accepted.
Print your name on the back of the bank draft or certified cheque.
Fees can only be paid in Canadian Dollar and Philippine Peso currencies although it is advisable to pay in Canadian Dollars to avoid currency fluctuation.
If you are paying in Canadian dollars, the bank draft or certified cheque should be addressed to the: Receiver General for Canada.
If you are paying in Philippine Pesos, the bank draft or certified cheque should be made payable to the: Embassy of Canada, Manila.
Cheques can be issued by any local or international banks or post offices. Bank cheques are valid for 6 months from the date they were issued, while PMOs are valid for only 3 months.
If bank drafts are issued from a bank in Canada in Canadian dollars, the "drawee" (also known as the clearance or correspondent bank) must be left blank.
If you are paying from abroad
Fees must be paid in Canadian dollars by bank draft to the Receiver General for Canada; drawn against any bank in Canada.
If your application is received at this office without the correct processing fee attached, it will be returned to you unprocessed. This can cause you significant delays, so calculate your fee carefully.
Cash payment is not accepted. We are not responsible for the loss of cash sent by mail or courier.
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