What do you call the payment method when a company transfers founds to another company?

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In the US, we usually call that a "wire transfer".

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It all depends on the jurisdiction (as in where? domestic/international? same/different bank) and the method used. 
There are several methods possible: Jason mentioned one.

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money order...
or easy way you should say 'transfer'

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I used your question as a Google keyword: it looks it is called "a two-sided transaction" or "inter-company funds transfer", but the matter is rather technical. bye

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funds = $$
to find-found-found

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