A new and previously hidden, ghostly image of Mary, Queen of Scots, has been discovered underneath the surface of a 16th century painting.

The spectral image of the Queen has discovered under the 1589 portrait of Sir John Maitland, 1st Lord Maitland of Thirlestane, a work attributed to painter Adrian Vanson, which hangs at an historic house near London.

The image, which "shows compelling similarities" to other near-contemporary depictions of the queen, was revealed by X ray photography.

The discovery is to be revealed in a new display at the Scottish National Portrait Gallery in Edinburgh this week.

Imprisoned by Elizabeth I from 1568, Mary was executed in England in 1587 – two years before the date on the overlying portrait of Sir John Maitland.

Mary’s recent execution may be a reason why her portrait was covered over, hidden or abandoned by the artist.

The portrait was one of several created by painters Vanson and Adam de Colone, two artists from the Netherlands who worked in Scotland at the end of the 16th century and the beginning of the 17th century.

They were examined by Dr Caroline Rae at the Courtauld, who recently undertook a collaborative research project in conjunction with National Galleries of Scotland (NGS).

Vanson’s portrait of Sir John Maitland (1589), the Lord Chancellor of Scotland, is part of the National Trust collection, and usually hangs at the Trust’s 17th century Ham House.

Dr Rae discovered the concealed portrait while conducting a technical examination using X-radiography (X-ray), a technique that can penetrate through paint.

The X-radiograph revealed the presence of lead white, depicting a woman’s face and the outline of her dress and hat beneath the upper layers of paint.

Dr Rae said: “The discovery of this hidden portrait of Mary, Queen of Scots is an exciting revelation, not only as it adds to our knowledge of 16th century Marian portraiture and patterns of commission at the time, but as it aids in illuminating our understanding of Adrian Vanson, a Netherlandish émigré artist who came to Jacobean Scotland to seek a new life and quickly ascended to the status of Crown painter.”

Sir John Maitland was Keeper of the Privy Seal in Scotland, Secretary of State to James VI and Lord Chancellor, and when the portrait was painted he was the second most powerful person in Scotland.

He was brother of William Maitland of Lethington who was Mary Queen of Scots’ Secretary of State.

Dr Rae's work was funded was a partnership between the Galleries and the Courtauld, and undertaken in both locations.

The discovery took place while she was examining several works by Vanson from the NGS collection, although the work itself belongs to the National Trust.

David Taylor, curator of pictures and sculpture at the National Trust, added: "Vanson’s portrait of Sir John Maitland is an important picture in the National Trust collection, and the remarkable discovery of the unfinished portrait of Mary, Queen of Scots adds an exciting hidden dimension to it.

"It shows that portraits of the queen were being copied and presumably displayed in Scotland around the time of her execution, a highly contentious and potentially dangerous thing to be seen doing."

Dr Rae was able to trace the outline of a woman, and based on other depictions of the Queen made in her lifetime, in particular her later years, concluded it was the monarch.

In particular, the face of the sitter for instance shows a strong resemblance to two miniatures by the famous English miniaturist Nicholas Hilliard (1547-1619), kept in the Royal Collection and the V&A Museum collection.

Other clues, like the sitter’s pose with her head tilted to the side and her hand at her waist with her fingers positioned as if holding something, the wired cap and square-necked gown, also accord with other portraits of Mary, including a work hanging at Blair Castle, Perthshire.

The National Galleries have also maintained this week that the iconic Monarch of the Glen painting was based on a stag in Scotland.

Stoke Park hotel in Buckinghamshire, previously a country house, believe the painting was based on a stag within its grounds during Sir Edwin's regular visits to the estate in the 19th century.

The NGS said Sir Edwin made annual trips to the north of Scotland and there is "no doubt" the Monarch of the Glen depicts a Highland setting.