You may use an employee’s national identification number (in Belgium the rijksregisternummer, also called the INSZ number) when that is necessary and legally permitted for personnel and payroll administration. But not as a general internal identifier.
What you need it for
Employers need the number, among other things, for social security declarations and for certain social and tax documents. In Belgium, for example, that is the Dimona declaration, which identifies the employee and establishes the link between employee and employer. For certain people without a national register number, Belgian social security assigns a BIS number.
Use the number solely for the statutory or administrative purposes for which you need it. The existence of an employment relationship does not give you a general right to use the number across all your HR systems.
The number is not a special category of data within the meaning of Article 9 GDPR, but it is a specifically protected national identification number. The Belgian data protection authority describes the national register number as an identifier whose use requires a statutory basis or authorisation; other member states have comparable restrictions for their national number.
What you do not do
So do not use the number as a general employee number, username, password, visible number on badges or general key to link files. Assign every employee a separate internal employee number.
Share the number only with parties that need it for a permitted purpose, such as your payroll provider or a competent public authority.
Map it
Map every storage location and every disclosure of the number to a statutory purpose, and remove it from systems in which an internal employee number is sufficient. Which other data from the identity card you may record is explained in Which data from an employee’s identity card may I record?
Legal basis
Use of the number falls under the principles of purpose limitation and data minimisation (Article 5(1)(b) and (c) GDPR) and relies on a legal obligation as its legal basis (Article 6(1)(c) and 6(3) GDPR). Article 87 GDPR lets member states set specific conditions for processing a national identification number, and Article 32 GDPR requires you to secure it appropriately. In Belgium, the Act of 8 August 1983 organising a National Register of natural persons and the social security and tax legislation apply on top of that.
GDPRWise maps your HR processes and systems, so you can confine sensitive identifiers to the places where they belong.