Media reported that police and divers in the Algarve region examined three disused wells in Vila do Bispo for eight hours on Thursday.
The area is about 16km from the Praia da Luz, where Madeleine disappeared on 3 May 2007.
Multiple investigators were at the scene with specialist diving equipment to examine the wells.
The investigation into Madeleine’s disappearance was renewed in June after German authorities announced they were investigating Brueckner, a convicted German child sex offender.