Is the word secretaria the same in Brazilian and European Portuguese?

No.

While both dialects use "secretaria" to refer to a formal administrative department (such as a "Secretaria de Estado"), there is a significant difference in typical usage. In Brazil, "secretaria" is commonly used to refer to the physical reception area or the front desk of a school, clinic, or small business. In Portugal, the word for that physical space is almost always receção. Furthermore, there is a distinction in the related word "secretária" (with an accent): in Brazil, it refers only to the person (the secretary), whereas in Portugal, it also refers to the piece of furniture (the desk).

Brazilian Portuguese Examples

1. Vou à secretaria da escola para pedir um comprovante. (I am going to the school office to ask for proof of enrollment.)
2. A secretaria do prédio está fechada hoje. (The building's reception is closed today.)
3. Deixe os documentos na secretaria, por favor. (Leave the documents at the reception, please.)
4. A secretaria de saúde anunciou novas vacinas. (The department of health announced new vaccines.)
5. Preciso ir à secretaria da clínica para fazer o check-in. (I need to go to the clinic's reception to check in.)

Continental Portuguese Examples

1. Vou à receção da escola para pedir um comprovante. (I am going to the school reception to ask for proof of enrollment.)
2. A receção do prédio está fechada hoje. (The building's reception is closed today.)
3. Deixe os documentos na receção, por favor. (Leave the documents at the reception, please.)
4. A Secretaria de Saúde anunciou novas vacinas. (The Department of Health announced new vaccines.)
5. Preciso ir à receção da clínica para fazer o check-in. (I need to go to the clinic's reception to check in.)