Investigators from Scotland Yard are waiting for an official agreement later this week, and hope to begin "operational activity" linked to the case in the near future.
Deputy Assistant Commissioner Martin Hewitt said he is "cautiously optimistic" that Portuguese and British officers can act soon.
He said: "I am cautiously optimistic that in the not-too-distant future we are going to start to see activity."
Mr Hewitt would not reveal what the operations will involve.
Police also revealed that they are now looking at five more cases in which young British girls were sexually assaulted during holiday home break-ins by a lone intruder in the Algarve.
One of these was in 2005 on a 10-year-old girl in Praia da Luz, where Madeleine, then three, vanished two years later.
Scotland Yard made public appeals to try to trace the paedophile last month, and so far more than 500 people have made contact with information.
Officers are now looking at a total of nine sexual assaults and three "near misses" on British girls aged six to 12 between 2004 and 2006.