After looking at the following article with the title "¿Cómo y cuándo se aplica la retención del 4% de IVA por flete?", I see that it most likely applies to a VAT withholding or sales tax withholding of 4% charged on freight:

http://ayudaeconta.globalpc.net/cuando-se-aplica-el-4-de-iva...

In addition, the article https://contarte.mx/que-es-una-retencion/ refers to "Retenciones por Fletes y Transportes".

More generally, you can also refer to it as "withholding tax," although this usually refers to income tax in particular. See https://en.wikipedia.org/wiki/Withholding_tax

I'm almost certain your source text is referring to the withholding of VAT or sales tax incurred on cargo. If you find mentions of it elsewhere in your text, then you could say "sales tax withholding" (for audiences based in countries using a general sales tax, such as the US, Canada, Australia, etc.) or "VAT withholding" (for audiences based in countries using a value-added tax, such as the UK, Ireland, South Africa, etc.).

An alternative is to say "tax withheld" or "no tax withheld." This way, you avoid specifying what tax it is. Saying "withholding" on its own is a bit strange and could mean various things, but then again, your source text does that too, so taking the context into account is important.

Translation options:

"E (Freight with 4% sales tax withholding)" or "E (Freight with 4% VAT withholding)" or "E (Freight with 4% tax withheld)"
"A (Freight without 4% sales tax withholding)" or "A (Freight without 4% VAT withholding)" or "A (Freight without 4% tax withheld)"

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Note added at 8 hrs (2020-05-11 20:11:18 GMT)
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As others have commented, flete refers to a freight charge (or freightage).

With this in mind, you can also translate it as follows:

E (Freightage with 4% tax withheld)
A (Freightage without tax withheld)