WIPO have recently issued Information Notice No. 29/2013 explaining how to pay official fees to them for registrations under the Madrid Protocol.
Those of you that deal with WIPO will know they can be a bit of bureaucratic organisation and the language of their Information Notice may be testament to this.
If you do not have a deposit account with WIPO - and many firms don't - then you will probably be required to transfer payment of official fees by bank transfer and this is why the Information Notice has issued. WIPO are regularly being short changed as users do not instruct their bank that they are to incur all the bank charges. This causes a headache and delay with WIPO and the user when it is necessary to request a second payment, which is usually fairly incremental.
If you have a deposit account with the UK Intellectual Property Office and you are filing a Madrid application through them as Office of origin then you can ask them to make the official fee payment (in Swiss francs) on your behalf and debit your deposit account. However, not many Offices of origin offer this service.
If you're based in Switzerland or Liechtenstein (or even in the Italian exclave of Campione d'Italia) then making payments in Swiss francs is not difficult. But most of us will not have a Swiss bank account.
Payment by credit card is not available at the time of filing Madrid Protocol applications because these are filed through an appropriate Office of origin and not WIPO directly. Nevertheless, I understand it is possible to wait for an Irregularity Notice to issue and then make payment by credit card through WIPO's E-payment tool. This is not exactly ideal as again it results in a delay.
WIPO also released their latest magazine 'Madrid Highlights' this week and this contained two fees related features.
Firstly, they will soon be launching a new on-line tool for filing Subsequent Designations with a credit card payment facility. This will not help with the initial filing of a Madrid application but I anticipate it making adding countries to an existing International Registration substantially easier - and hopefully quicker.
Their Madrid Tips section also explains some scenarios regarding the official fees payable for renewals. These can seem ridiculously complicated at times although if you can use WIPO's E-Renewal tool this should auto-calculate the correct fees for you.