The parents of Madeleine McCann made a pilgrimage to Portugal’s holiest site yesterday to pray for a miracle to bring their daughter home as the three-week police investigation into her disappearance appeared to be making little progress.

Kate and Gerry McCann’s visit to Fatima was particularly poignant as the 90th anniversary of the vision of the Virgin Mary earlier this month had coincided with the fourth birthday of their missing daughter.

The physical agony of the penitents who approached the shrine of Fatima on their knees was mirrored by the mental anguish on the face of the McCanns as they entered the Chapel of Apparitions. However, the couple began to smile as they were showered with kisses and hugs after slipping into the back of a Mass, on the exact site of the apparitions, in time for the sharing of the Peace.

Mrs McCann was again clutching Madeleine’s favourite soft toy cat, which she has carried everywhere since her daughter was abducted from her bed in their holiday apartment in Praia da Luz 21 days ago. In her hair were the green and yellow ribbons that have become a symbol of the campaign to find Madeleine.

The couple, both 38, from Rothley, Leicestershire, later spent 30 minutes in a side-chapel for private prayers before returning to the square in front of the basilica to light candles for Madeleine. Maria Arlete, who handed two candles to the couple, said: “People are looking for miracles. Maybe that’s the only thing left, a miracle.”

Returning to the main chapel to say the Rosary, the couple sat beside the marble pillar marking the spot where three shepherd children had seen visions of the Virgin Mary in 1917. Monsignor Luciano Guerra, rector of the shrine, made several references in Portuguese to Madeleine’s disappearance, referring to her abductors as “vultures”.

As the McCanns left the chapel the 1,000-strong congregation ignored the strict rule of silence to break into spontaneous applause and to inundate them with gifts of religious icons and flowers.

Despite the presence of the television cameras and reporters, who have made the McCanns the most famous couple in Portugal, they said they had drawn enormous strength from the visit. While Mrs McCann’s religious belief is long-standing, her husband in particular is said to have found new faith in recent days. e millions of pilgrims who visit the shrine at Fatima each year. Yesterday was the first time that she had left the Algarve since Madeleine was abducted.

Both Mr and Mrs McCann are preparing to travel across Europe to raise awareness of their daughter and to promote their campaign website, www.findmadeleine.com .

They returned to Praia da Luz to learn that detectives leading the hunt for their daughter had reinterviewed two of the “witnesses” in the investigation. Michaela Walc-zuch, the girlfriend of the prime suspect, and her estranged husband, Luis Antonio, spent several hours being questioned at the headquarters of the Policia Judiciaria (PJ) in Portimão.

However, the police investigation appeared to be foundering yesterday after reports that tests on hair, sweat and fibre traces discovered at the apartment where Madeleine disappeared while sleeping between her brother and sister had so far yielded no clues.

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