Thank you for the complete sentence. Now we know :

Where : Dans le présent guide, par méthode,

When : lorsqu’il est fait référence aux dispositions spécifiques (du règlement général de X ou du règlement Y) applicables aux sociétés de gestion de portefeuille ,

What : il est indiqué l’expression « pour les sociétés de gestion de portefeuille soumises au titre Ier bis du X pour leur activité de gestion de FIA

It certainly helps to make sense of how the problem term fits in! The important elements are:
“…par méthode… il est indiqué…”
As I read this, “par méthode” simply means “always” here. It is something which is to be done systematically, automatically, each time.


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Note added at 1 day26 mins (2015-06-20 10:24:14 GMT)
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As in "methodically".

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Note added at 1 day29 mins (2015-06-20 10:27:12 GMT)
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Now it is possible to make sense of the suggestions you had come up with yourself, by the way! It really was essential to have the full text. My suggestions might work. It pretty much depends how the rest of the sentence is worded. I like the idea of "as a rule" too, suggested by Daryo.

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Note added at 1 day32 mins (2015-06-20 10:29:47 GMT)
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You could also use :" must, should shall". Adopting a verbal solution to incorporate the idea could ork well too.