Mr Sousa, a spokesman for the Policia Judiciara, said evidence of her abduction may have been contaminated because more than 20 people had gone into the McCann's Mark Warner holiday apartment on the night Madeleine disappeared.
He told a Portuguese newspaper: "The presence of so many people - especially in the room where the little girl slept with her brother and sister could have at least complicated the work of the forensic team."
He added: "At the very worst they would have destroyed all the evidence. This could prove to be fatal for the investigation."
The McCanns were said to be "dismayed" by Mr Sousa's remarks.
A source close to the family said: "It's insensitive at the very least. Of course the family are going to search the apartment.
"If your child goes missing, you search under the beds, in the wardrobes, behind the doors, everywhere.
"It's inevitable that there were people in the bedroom. Even if what the police are saying is true, it's very unhelpful to say it publicly."
Parents Kate and Gerry McCann, have held onto their Catholic faith throughout their ordeal of searching for their daughter, regularly attending a local Catholic church as well as recently travelling to Rome to meet Pope Benedict XVI, who prayed for the missing British girl.
Mr McCann, who attended Sunday mass yesterday, said that like his birthday two weeks ago, he was barely aware of Fathers' Day.
The 39-year-old said it was too painful to remember life as it was a year ago: "I can't think about last year and how we spent it, I honestly can't.
"I can't really think about anything else, other than how we can help try and get Madeleine back."
This Friday, the McCanns are planning on releasing 50 balloons from 50 countries to highlight the fact their daughter will have been missing for 50 days.
Germany, France, Australia, Dubai, Canada, America and El Salvador are among those places expected to take part.
Mr McCann said: "We will probably have 10 centres in the UK - like Glasgow, Liverpool, Leicester - as well as Ireland and Guernsey where we have friends, and Kate and I will do the Praia da Luz one.
"We are going to tie it in with other missing kids. We were anxious about going to their countries and asking for help finding Madeleine but they have said 'what you are doing is amazing and it is helping us'."
