Authentication with the AEAT requires an electronic certificate accepted by the AEAT, whose NIF is the same as that of the company. Citing the AEAT:

The presentation can be made by the taxpayer, a representative of this process or a social worker, who must have a recognized electronic certificate. Applications that send information to web services must be authenticated with the client's electronic certificate. Therefore, the use of the services requires having installed a recognized electronic certificate accepted by the Tax Agency, in the computer from which the information is sent. This certificate may be of a Personal or Legal Entity. All NIFs must be validated against the AEAT Centralized Database.

More information:

http://www.agenciatributaria.es/static_files/AEAT/Contenidos_Comunes/La_Agencia_Tributaria/Modelos_y_formularios/Suministro_inmediato_informacion/FicherosSuministros/V_06/SII_Descripcion_ServicioWeb_v0.6_es_es.pdf

On the admitted certificates:

http://www.agenciatributaria.es/AEAT.internet/Inicio/Ayuda/Certificado_electronico/Como_obtener_un_certificado_electronico/Entidades_emisoras_de_certificados_electronicos_/Entidades_emisoras_de_certificados_electronicos_.shtml

About the model of Representation to use a certificate for more than one company:

http://www.agenciatributaria.es/static_files/AEAT/Contenidos_Comunes/La_Agencia_Tributaria/Modelos_y_formularios/Formularios/Modelos_de_Representacion/MODELO_REPRES_SUMINISTRO_FACTURACION.pdf

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