The remains of the rare Atlantic whale which died in the River Thames will be given to the Natural History Museum for research, it was announced today.

The young northern bottle-nosed whale was watched by millions on television around the world as she struggled to survive in the shallow waters of the river. Initially spotted on Friday morning, her presence drew thousands of spectators who lined the banks of the Thames, cheering on attempts to rescue her.

But despite all efforts to guide the distressed mammal to safety, the 19ft (5.8m) whale died at 7pm on Saturday night.

Since then, Dr Paul Jepson, veterinary pathologist for the Zoological Society of London (ZSL) has been carrying out a post-mortem examination.

The whale was initially examined at the spot where she died at the dockside in Denton, near Gravesend, Kent. Today, the carcass was taken to the ZSL’s laboratories in London’s Regent’s Park but the results are not expected until Wednesday.

Once Dr Jepson has completed his study, the bones will be cleaned and preserved at the museum for scientific research.

Information gleaned from the whale will be used in the UK’s Marine Mammal Strandings Project which is co-ordinated by ZSL and the Natural History Museum. The project investigates the causes of mortality in UK marine mammal species off the UK coast.

The attempt to rescue the whale, by the British Divers Marine Life Rescue group (BDMLR), was followed around the world, and cost the volunteer organisation an estimated £100,000.

Such was the interest, that a red plastic watering can used to douse the whale as it was transported by barge towards the North Sea is being auctioned on the eBay website to raise money for the organisation. By late afternoon today, bidding had reached £490.

But the BDMLR learnt today that it would not have to pay £300 of parking tickets that its "marine medics" incurred after abandoning their cars near Westminster bridge to mount the rescue operation.

A spokesman for Westminster Council said the fines would be waived for all members of the rescue team. "We have told them that they do not need to go through the appeal process," he said. "They just need to give us the codes of the tickets and the names of the drivers and they will be cancelled."

The results of the post-mortem examination will be announced on Wednesday, but there is increasing speculation that sonar from Royal Navy vessels could have disorientated the animal.

The Scottish Tory MEP Struan Stevenson said: "I suspect that the post-mortem will find that the whale’s auditory system will have been damaged.

"Whales use sound as we use our eyes. If Low Frequency Active Sonar, or LFAS, is used within 50 miles it can cause massive damage to the animal’s organs.

"Nuclear submarines use LFAS and it demonstrates a frequency underwater of 180 decibels. It could be that happened to a pod of whales and led to this animal finding its way right up the Thames. This also comes on the back of 20 dolphins being found on beaches in the South West of England."

But the Ministry of Defence consulted a noise specialist and dismissed the claims as pure speculation. An MoD spokesman said they had consulted Vibrock Ltd, an independent company specialising in vibration monitoring and control. The company has studied the effects of noise and vibration from the Shoeburyness range, at the mouth of the Thames, for over a year.

Tim Wilton, from Vibrock, said: "It is inconceivable that the effects of activities at the range could have contributed to this unfortunate incident. The impact of the MoD’s work on the marine environment is minuscule compared to everyday shipping activity in the area."

Tony Woodley, from BDMLR, said it was too early to blame human interference. "It is generally accepted that the animal was lost, being away from its normal environment of the deep sea Atlantic," he said. "But until the post-mortem is completed we can’t tell if it had major internal problems or not."

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