Sir Bernard Hogan-Howe said it would have been "very difficult" for officers in Praia da Luz to know whether they were dealing with a serious crime immediately after the little girl vanished in May 2007.
He said: "I think sometimes these things at the beginning can be very difficult to deal with, you don't know exactly if the child has just wandered off. It can be very difficult to know if you've got a very serious crime.
"I'm sure for them that must have been a challenge. Anybody can go back after two, three, five, six years and say 'why didn't you do that'?
"That's easy in hindsight.
"We don't like it when it happens to the Met, and I'm certainly not going to do it to the Portuguese. What I'm determined to do is to work together to make sure we've got the best chance to now try to get to the bottom of this terrible tragedy.
"There is a poor family there, who've got the torture of not knowing whether their daughter is alive or not."
Scotland Yard is now running its own investigation into what happened to Madeleine, who was three years old when she missing from a holiday apartment as her parents Kate and Gerry, who is from Glasgow, dined at a nearby tapas restaurant with friends. The Portuguese inquiry was shelved in 2008.
Sir Bernard said the discovery of two blonde-haired, blue-eyed girls living with Roma families in Ireland and Greece has not had any "direct impact" on the investigation, but added: "It looks like there's a possibility that around the world there are occasions when people steal children and keep them.
"And I'm sure in one sense that's what the McCanns must be hoping, that at least their child is alive.
"The other possibility is that sadly she's not alive, and either way we want to try and end the torture that they're going through."