Portugal's investigative Judicial Police (PJ) had said on Monday they would execute search warrants between Monday and Friday at the behest of the public prosecutor's office in Germany's Braunschweig, which in 2022 formally identified German citizen Christian Brueckner as an official suspect in the case.
A source involved in the search operation said the targeted area was "vast" with police using ground-penetrating radar across several hectares.
Portuguese officers were following instructions from German police under a European Investigation Order.
The scale of the searches could be the most extensive since the initial investigation was closed in 2008.
Fresh but relatively focused searches were ordered by Portuguese, United Kingdom and German police of scrubland, wells and reservoirs in 2014, 2020 and 2023.
None of these searches were confirmed to have yielded significant evidence.
Reuters footage showed uniformed PJ officers on a cordon on a dirt road in Atalaia - a neighbourhood of Lagos municipality - waving through unmarked vans and cars with German licence plates from the city of Wiesbaden, where the Federal Criminal Police Office (BKA) has its headquarters.
The BKA is assisting Portuguese law enforcement with "criminal procedural measures," Braunschweig prosecutors told Reuters, declining to provide further details.
The occupants of one of the German vehicles wore bucket hats, clothing with camouflage patterns and covered their faces with bandanas.
A van belonging to Portugal's Maritime Police also arrived.
That force has jurisdiction over coastal areas and took part in previous searches of beaches, wells and reservoirs using specialist divers.
The road the police cordoned off is located close to a golf course and less than 1km from the beach.
The search area was close to a property that Brueckner lived in, a neighbour told Reuters in 2020, although when was unclear.
Madeleine went missing on May 3, 2007 while on holiday with her family in the Algarve town of Praia da Luz, sparking a frenzied search and gaining the attention of the world's media.
She has never been found.
German police said in June 2020 that Madeleine was assumed dead and Brueckner, in his 40s, was probably responsible.
He has denied responsibility.
Brueckner, a convicted child abuser and drug dealer, is behind bars in Germany for raping a 72-year-old woman in the same area of the Algarve.
His sentence runs until September, meaning he is set for release unless prosecutors find enough evidence to charge him over Madeleine's disappearance.
On January 17, Sky News quoted the German prosecutor investigating Madeleine's disappearance as saying there was currently no prospect of charges being brought against Brueckner.
