Prince Harry was in deep water today - if only literally - as he participated in a Royal Navy diving exercise while police investigated the shooting of a pair of protected birds on the Queen's Sandringham estate.

The Prince, who has been questioned by police, was in the area at the time of the shootings last week but denies any involvement, a Clarence House spokesman confirmed today.

Police said this morning that they are preparing a report for the Crown Prosecution Service, which will decide whether a case should be brought. They have questioned three men over the incident, which could lead to a prison sentence of up to six months or a £5,000 fine.

Shooting experts said that whoever killed the hen harrier birds of prey would have to be "stupid or ignorant" to confuse them with legitimate targets.

Jeffrey Olstead, of the British Association for Shooting and Conservation, said that it would be "extremely difficult" to mistake a hen harrier with a game bird or a pest species because of its distinctive shape, colour, flight and speed. Shooters at Sandringham would be looking for partridge or pheasant, he said. "Their flight pattern is very fast, direct, and with fast wing beats. Partridge are small, dumpy and keep low to the ground. Pheasant will go higher, but they have a long tail that give a distinctive outline. The outline of a harrier is utterly different. It's flight pattern is different - they float around in the air. They glide using thermals."

He added that disciplined shooters are taught never to shoot anything unless they can positively identify it. Other legitimate targets likely to be on the estate include duck, woodcock, snipe, magpie or pigeon, but all are distinct from the harrier, he said. "It is difficult to see how a mistake could have been made. Perhaps if someone were shooting into the sun. Accidents can happen. But basically you would expect someone shooting live quarry to recognise what it was they were shooting. Or at least have the discipline not to shoot until they were sure. It's more likely to be stupidity or ignorance."

Royal officials said Prince Harry and one of his friends were “in the area” when the birds were killed on the Sandringham estate near King’s Lynn, Norfolk, late last Wednesday. They said the Prince “no knowledge” of the alleged shooting and could not help police.

Officials would not say what the Prince and his friend were doing at the time nor whether they were accompanied by officers from the Metropolitan Police’s Royal Protection Squad.

They also refused to say whether the Prince had come forward to make himself available. A spokeswoman for Clarence House said: "Because Prince Harry and a friend were both in the area at the time, the police have been in contact with them and asked them if they have any information that could help. Unfortunately, they had no knowledge of the alleged incident.”

A spokesman for Norfolk Police said: “The investigation is ongoing. We are interviewing three people and will be making a report to the Crown Prosecution Service for a decision.”

The Queen, Prince Harry’s grandmother, is the patron of the Royal Society for the Protection of Birds (RSPB). RSPB officials say they are “disappointed” such an investigation is taking place on a royal estate.

Staff said the shooting was reported by a conservation warden monitoring harriers. They said the warden had seen the birds hit and heard a shot but had not seen the shooter.

Sources said police had not found the carcasses of the birds.

A spokesman said it was notoriously difficult to find people responsible for shooting protected birds because of the isolated areas the birds were found in.

The RSPB criticised the Sandringham estate in November last year when a gamekeeper was fined £500 for illegally using a trap. Dean Wright, 26, of Anmer, Norfolk admitted setting a trap in which a tawny owl got caught.

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