Officers also began using ground-penetrating radar equipment, which looks for signs of disturbed earth.
Met Police said requests to search two other sites had been granted, and has also asked to extend the current search of scrubland by an extra seven days.
Madeleine was three when she went missing in Portugal in 2007.
British and Portuguese officers have continued a search of 15 acres of cordoned-off scrubland at the Algarve resort. All search efforts on Wednesday have now finished.
The day's main search activity took place within two white tents which were erected on the scrubland, and forensic officers wearing blue overalls and face masks were seen walking in and out of them.
The BBC understands that the tents were put up over a hole in the ground - possibly a disused well - and officers were seen filling buckets with earth, which were then placed into a wheelbarrow. No radar equipment was used near these tents.
Earlier in the day, officers in Metropolitan Police uniforms were driven to a separate part of the cordoned-off area, where they were joined by Portuguese police and local forestry workers with strimmers.
A man in plain clothes wheeled the radar equipment onto a section of ground that had earlier been cleared.
Officers from the Met and South Wales Police were also working with sniffer dogs and using spades to help sift through the undergrowth.
They were being overseen by the Met's Det Ch Insp Andy Redwood, the senior officer investigating the case.
The painstaking search of a site in the resort of Praia da Luz has been continuing, with a forensics officer joining the police team on Wednesday.
Work seems to have been concentrated in one particular area, with police going back and forth to a section of land at the perimeter of the site. Two tents have been erected here - it is unclear if that is to prevent the media from seeing what is being done or to provide shade.
While the police can't be seen from the beach, which is packed with holidaymakers enjoying the Algarve sun, everyone here seems all too aware of the investigation.
Christina, a 35-year-old from Bournemouth on holiday with family and friends, said: "We walked down here last night and it was quite scary seeing so many police around.
"The atmosphere here feels a bit flat because of what's happening. When you're on holiday you don't want to see police around but it's completely understandable."
Her friend Suzi, 34, said: "It's a bit of a shame because it's a lovely place and this does seem to have had an effect on the economy and on the people here.
"But if that was your child, you would want everything possible to be done."
Several people the BBC spoke to had not known, before arriving at the resort, that it was the place where Madeleine McCann was last seen.
Josie, 29, from Exeter, on holiday with her partner and one-year-old son, said: "It brings it home to you, being here - it makes it feel more real.
"We didn't realise when we booked that this was the place. It wasn't until I saw my dad I knew because he told me. I don't know if we would have come here otherwise.
"But police have to do what they have to do. We all want the best for the family."
Portuguese police sources told the BBC the search might be extended if there was a significant find. Officers are believed to have been surprised by the difficulty of the terrain, while the police also need to consider the disruption to local residents.
On Wednesday morning, the national Portuguese newspaper, Correio da Manha, reported that there would be a search of the sewage network around the Ocean Club, where the McCann family was staying when Madeleine disappeared.
Officers were expected to use cameras linked to fibre-optic cables, the paper said. It also reported that the bones of cows and pigs had been unearthed by the search on Tuesday.
A Metropolitan Police spokeswoman said there would be no running commentary on the operation.
Two sniffer dogs have been provided by South Wales Police for the search.
The Met launched a fresh investigation into Madeleine's disappearance last July, codenamed Operation Grange.
In March, they said they were seeking an intruder who sexually abused five girls in Portugal between 2004 and 2006.
Detectives said the attacks had happened in holiday villas occupied by UK families in the Algarve.
And last month Scotland Yard said a "substantial phase of operational activity" in Portugal would start soon.
Police investigating the disappearance of Madeleine McCann have focused their efforts on a patch of land on the third day of a fresh search in Praia da Luz.