A five-man team made up of British and Portuguese officers were seen lifting three manhole covers and lowering a camera attached to a long pole down them.
One of them wrote notes in a book as they looked inside, around 20ft from where ground-penetrating radar equipment was used in the Algarve resort of Praia da Luz yesterday.
One of the men also lowered a tape measure into the drains, which were just inside the cordon set up around the large area of scrubland.
The search of the area for clues to what happened to Madeleine, who disappeared aged three in May 2007, is likely to go into a second week after British police applied to the judiciary to spend an extra seven days there.
It is not clear whether they will work over the weekend and nothing is expected to be carried out on Tuesday as it is a public holiday.
The team searching the drains then moved away out of sight of the dozens of TV crews and press watching from the other side of the cordon.
Earlier the Met's Detective Chief Inspector Andy Redwood, the senior officer investigating the case, looked on as a group of his officers used pickaxes and spades to clear leaves and grass from the same area during a fourth day of investigations at the site.
The area being searched, which is a few minutes' walk from the Ocean Club resort apartment where Madeleine and her family were staying, saw officers focusing their investigations on a hole which had been previously covered by undergrowth.
But it is understood nothing of significance was found there, with bones found identified as those of animals.
Sniffer dogs from South Wales Police have also been used on the site, and were seen with their handlers earlier today.
An officer in Met Police uniform was seen digging a hole in an area where the radar equipment was used yesterday.
The hole was then covered with a white tent and an officer was seen using a small paintbrush on some of the large pile of earth that had been dug out outside.
The area was marked with a small yellow flag, which have been dotted around the site at points of interest to the police.
Other teams appeared to be carrying out work out of sight of the police cordon, which surrounds the area and is being guarded by armed officers day and night.