The site was just nine miles from the resort where the four-year-old was abducted.
Police vans, one carrying sniffer dogs, had moved in at first light in the village of Arao, not far from Praia da Luz.
It is now 43 days since the girl was taken from her bed as she slept in the Algarve resort.
Two days ago, Portuguese police were told about a letter alleging that Madeleine's remains were under rocks in this area.
The information was sent to a Dutch newspaper, The Telegraaf, and claimed her body was just seven metres from the road.
Police did not treat the search as a priority on Thursday but "with all the media attention the letter had got, they thought they better have a good look", he added.
The village which was cordoned off lies just north of the main road from Praia da Luz to Faro.
Meanwhile, Kate and Gerry McCann have been focusing on finding their daughter alive.
Mr McCann condemned De Telegraaf for publishing details of the letter before police were given a chance to investigate as "insensitive and cruel".
Dutch police said the letter was taken seriously because it was similar to information sent to the same newspaper last year, giving details of the rough location of the bodies of two missing Belgian girls.
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