Leading museums have lost nearly 200 items in recent years worth more than half a million pounds, The Sunday Telegraph can reveal.

The Science Museum has lost 42 items since 2000

Details obtained under the freedom of information act show that museums including the Natural History Museum, the Science Museum, the Imperial War Museum and the Royal Armouries have lost 198 items since 2000.

Items that have disappeared from the museums include a Victoria Cross (VC) medal belonging to one of the Second World War's most decorated soldiers, dozens of antique rifles and pistols, a painting worth £200,000 and a collection of 14 microscopes worth £157,000.

The museums' losses total £501,995. However, the value of many of the lost items are unknown, with the total value therefore likely to be far higher.

The Royal Armouries, which has museums in London, Leeds, Fort Nelson, Portsmouth, and a branch at the Frazier International History Museum in Kentucky, USA, has lost 143 items worth £21,295 since 2000.

The items include pieces of armour, antique rifles, pistols and muskets. Only 24 of the 143 missing items have been recovered.

The Science Museum in London has lost 42 items, including 14 microscopes worth a total of £157,000, which were all stolen from their display cabinets on the same day in July 2005.

Other items that have gone missing from the museum include 13 significant scientific articles from a number of periodicals valued at £23,300, which were cut out of a volume in the Science Museum Library in November 2005.

A clairvoyance crystal which once belonged to John Dee, the personal astrologer and astronomer to Queen Elizabeth I, valued at £40,000, also went missing from the Science Museum in 2004. It has since been recovered by police.

The Natural History Museum has lost three items, including a 70-million-year-old coprolite, or dinosaur dung, which was reported as stolen to the police in 2006, and two conodonts – extinct eel-like creatures dating from the Late Triassic period – which went missing in March 2008. Their value is unknown and none has been recovered.

Items missing from the Imperial War Museum include two sets of cam gears from a 1945 Rolls-Royce Aero engine worth £30,000 and a VC medal and medal bar which was awarded to Captain Charles Hazlitt Upham during the Second World War. Captain Upham, a soldier from New Zealand, earned the VC twice during the Second World War – the only soldier to do so.

The medal was stolen from the National Army Museum in Waiouru, New Zealand, while it was on loan from the Imperial War Museum. It was later recovered in February 2008.

While the Imperial War Museum has withheld information regarding the value of the stolen VC, recent auctions of VCs earned during the Second World War have fetched up to £250,000.

A painting worth £200,000 by Bonaventura Peeters the Elder, a Flemish Baroque painter, was stolen from the National Maritime Museum in Greenwich in July 2007. The artwork, entitled Sunlight on a Stormy Sea, c. 1640, was recovered five months later.

The Sunday Telegraph recently revealed that works of art worth thousands of pounds have also gone missing from the Government Art Collection in the past year.

Jeremy Hunt, the shadow culture secretary, said: "These figures show that sadly it isn't just the Government Art Collection that needs to improve its management of our national collections. Losing items on this scale undermines our reputation as one of the best countries in the world at preserving, restoring and looking after fine art.

"Improving security and inventory management may seem a boring thing to do, but it needs to be a top priority."

Roy Clare, the chief executive of the Museums, Libraries and Archives Council (MLA), which promotes best practice in museums, said: "Millions of people visited leading museums and galleries in the past few years. In relation, the level of loss is low.

"Museum staff balance the risks of theft against the need to display and interpret objects, and to engage audiences of all ages and backgrounds.

"Every theft from a museum or gallery is taken very seriously and investigated by the institution concerned. The MLA offers professional security advice, and publishes guidance for improving standards and managing risks.

"There is a delicate balance between allowing the public access to the UK's outstanding collections and protecting the national treasures they represent. In the overwhelming majority of cases this balance is managed with style and a huge degree of professionalism in the UK.

"However, where lessons can be learned the MLA is keen to learn from them and to be on hand to assist and advise those responsible for managing the front-line issues."