Kate and Gerry McCann were named as "arguidos" - or formal suspects - four months after their daughter vanished from their holiday flat in the Algarve resort of Praia da Luz.
Alipio Ribeiro, national director of the Policia Judiciaria (PJ), has revealed he believes there "perhaps should have been another assessment" before this happened.
The PJ is leading the investigation into what happened to Madeleine on the night of May 3.
In an interview with Portugal's Radio Renascenca, to be broadcast on Sunday, Mr Ribeiro stressed he did not give his officers orders about who should be named an arguido.
But he said there was a "certain hastiness" in making the McCanns suspects.
The couple's spokesman, Clarence Mitchell, today welcomed the senior officer's comments and called for them to be formally cleared.