This doesn't refer to a land registry, which registers land, but to a registry of entities engaged in activities that render them liable for so-called special and environmental taxes; each registry corresponds to a particular area or territory under the authority of one of the regional "oficinas gestoras de impuestos especiales".

There are, in all, 56 such oficinas gestoras in Spain. The country has 50 provinces. It's mostly one per province, but a few provinces (e.g. Asturias and Pontevedra) have more than one. Here's the full list:
http://noticias.juridicas.com/base_datos/Fiscal/o3482-2007-e...

So then the "registro territorial" is the registry for the territory under the authority of one of these provincial or sub-provincial agencies.

The Tax Agency (AEAT) itself simply calls it the "territorial registry", and I can't really see a good alternative to that:

"Approval of types of card documenting registration with the Territorial Special Taxes Registry"
http://www.agenciatributaria.es/AEAT.internet/en_gb/Inicio/L...

Here's their page on registration for the fluorinated gas tax. Click on "Castellano" at the top to see the Spanish version:

"It is determined that the parties subject to this tax, as well as the waste managers and beneficiaries of tax exemptions and reduced tax rates, must register in the territorial registry corresponding to the location of their establishment, or else where their registered tax address is located."
https://www.agenciatributaria.es/AEAT.internet/en_gb/Inicio/...

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Note added at 2 hrs (2018-07-09 01:56:51 GMT)
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The alternatives to "territorial" that spring to mind are "regional", "provincial" or "local". But none of these is really accurate. The word "regional" in Spain is normally applied to a highly level of territorial division corresponding to the autonomous community (17 of these in Spain). "Provincial" is not quite right for the reason explained: in a few cases there is more than one per province. And "local" normally applies to the municipal level.

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Note added at 2 hrs (2018-07-09 01:57:36 GMT)
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Sorry, a "higher" level, not a "highly level" (in the added note).

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Note added at 4 hrs (2018-07-09 03:56:32 GMT)
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My first link is to Anexo XLIII; I just tried it and it didn't jump to that point as it should have done.