A UNIQUE pair of flags that were flown at the Battle of Trafalgar, and which were housed in St Mary the Virgin, Selling, in Kent, will be sold to the National Maritime Museum at Greenwich, after a faculty was granted by the Commissary General of Canterbury.

One is a Union flag that measures more than seven by nine feet, which flew from a British ship of the line, HMS Minotaur, one of the ships in Nelson's own division at Trafalgar. Nelson had specifically ordered on 10 October 1805 that "When in the presence of an enemy, all the ships under my command are to bear White Colours, and a Union Jack is to be suspended from the fore-top-gallant stay."

The other flag is an Austrian ensign, which is more than seven feet by 13 feet, and is from the locker of the Spanish ship Neptuno, which was disabled and captured by the Minotaur.

The flags were initially in the possession of Captain Stephen Hilton (1785-1872), who, at the time of the battle, was Master's Mate on the Minotaur. After the battle, he settled in the village of Selling, and with his prize money he built a house that became known as Trafalgar House. Another part of his prize comprised the two flags. The flags were passed down his family, and, in 1930, Melville Hilton-Simpson gave them to the church.

On 23 August 1930, a local newspaper reported that a memorial chapel had been dedicated at the church in honour of the "Reverend William and Mrs Hilton-Simpson, parents of Captain Melville Hilton-Simpson"; that the family had united in the furnishing and adornment of the chapel; and that the two flags had been hung in the chapel.

The flags remained in the church until 1994, when they were taken to an expert conservator at her home in Sandwich, and they remained there until some time in 2010 or 2011. They were then removed to Canterbury Cathedral Treasury, and are now extremely fragile. They had at some point in the past been backed with an inappropriate material, which needs to be removed with great expertise.

The parish began to explore the possibilities for disposal of the flags because it was felt that they could not be displayed, owing to their value, and because they would deteriorate further unless displayed in suitable environmental conditions. There was also concern about the security implications of returning them to the church, and the probability that such a return would spell the end of the current practice of leaving the church unlocked.

An expert valuation by specialists in nautical works of art at Bonhams suggested a sale estimate of £100,000 to £150,000 for the Union flag, and £5000 to £10,000 for the Austrian flag.

Several options were put forward as to where the flags could go. The Commissary General, Morag Ellis QC, decided that the best option was the National Maritime Museum, because its "credentials as expert conservators and curators of naval history are beyond dispute". It had both the expertise and the resources to care for the flags. As a national museum, it operated under statutory powers and constraints, which meant, in particular, that the flags would be held permanent- ly, and entry to the museum was free.

The Union flag would be displayed in the museum's new permanent "Navy, Nation and Nelson" gallery, which will have the largest Nelson collection, including the uniform that Nelson was wearing when he was fatally wounded. The museum already had a collection of objects relating to the Minotaur, including Captain Mansfield's sword and medal, and the original plans for the ship, which was built in Woolwich dockyard.

The Austrian flag will probably be kept for much of the time in the museum's archive, but the museum would be obliged to make it available for viewing upon request. It would also form part of the online archive, and its acquisition and restoration would be publicised online.

The Commissary General emphasised that the grant of the faculty for the disposal of the two flags would not "set a precedent as a matter of law, and it [was] not intended to provide any kind of encouragement to parishes to dispose of treasures". This case was "exceptional", she said, and the faculty was granted owing to the necessity of ensuring proper care for the flags in the future, and the desirability of divesting the parish of responsibility for the physical safety and condition of the flags.

The terms of the faculty included the provision by the museum of replica flags. The DAC, and a representative of the Hilton family, are to be involved in discussions about the precise nature of the proposed duplicates.