Every day, hundreds of pilgrimages to Angkor Wat come to an end without a single glimpse of a centuries-old secret, one that long ago faded into the ancient temple walls.

By using digital photography and computer analysis, researchers recently discovered elaborate depictions and murals of elephants, trees, boats and Buddha that are otherwise invisible to the naked eye, erased from plain sight by years of weathering.

From the remaining traces of pigment, an Australian and Cambodian archaeology team was able to reveal more than 200 paintings that once graced the monument’s innermost galleries.

“These paintings literally faded into obscurity,” said Noel Hidalgo Tan, a rock art scientist at the Australian National University in Canberra who led the research project.

Locals and some archaeologists claim to have known about the existence of Angkor Wat’s paintings for years, but until Tan’s research team published their findings in March, no one had ever paid them much attention, let alone used image-processing techniques to discover the full extent of the artwork.

Tan first noticed subtle traces of red paint in 2010 while strolling through Angkor Wat on a lunch break from a nearby archaeological excavation. He took a few pictures of the faded outlines and decided he would at some point digitally enhance them to look for more details. Two years later, Tan returned to the 12th-century temple to complete the documentation as a side project to his doctoral thesis research.

“As a rock art researcher, I’m used to picking up traces of pigment, but when we put the images in the computer, I was very surprised at how elaborate these paintings are,” Tan said.

Using a technique called “decorrelation stretch analysis”, which increases colour contrasts otherwise impossible to see, Tan and his research associates from the Apsara Authority, the body that oversees and manages the temple complext, unveiled hundreds of paintings unlike any others found in Cambodia.

“Generally, paintings in Cambodia are on monastery walls and depict the life of the Buddha or Jatakas [stories of Buddha’s other lives] . . . But here in Angkor Wat, they are mostly images from people’s daily life,” said Im Sokrithy, an archaeologist and deputy director at the authority.

Mixed in among the animals, floral patterns, geometric designs and men on horses, the Angkor Wat images also contain two notable paintings that give researches a rough idea of how old they might be: a masted ship suggests contact with Europe had been established at the time, and an image of a sitting man resembling Buddha indicates the paintings were made after the Hindu temple was converted into a Buddhist site.

Built in the 12th-century under the reign of Suryavarman II, Angkor Wat was initially dedicated to the Hindu god Vishnu and was made the capital of the ancient Khmer Empire. Though one of the paintings depicts a Hindu monkey god, Tan believes the paintings he revealed stem from the post-Angkor period, possibly the 16th-century when King Ang Chan converted the temple to Buddhist use and commissioned a restoration project.

“What these paintings do is attest to the continued vitality of Angkor during this period of history, which is something that’s too often ignored or downplayed,” said Damian Evans, an archaeologist and director of the University of Sydney Robert Christie Research Centre in Siem Reap. “Our understanding of this ‘middle period’ of Khmer history is extremely poor, and almost no archaeological work has ever been done on it.”

One of the most detailed works in the Angkor collection depicts all the instruments of a pinpeat, a traditional orchestra complete with gongs, oboes, xylophones, drums and flutes, evidence researchers said could indicate the markings are more than simple tokens of long-ago visitors.

“People had dismissed the visible pigment as marks of vandalism. While I agree that some of these paintings could be random graffiti, many of are done so systematically and elaborately that they suggest deliberate action and planning. You couldn’t just do all these scenes in a day,” Tan said.

Now that Tan and the Apsara Authority have created a catalogue of Angkor’s paintings, they hope the work will encourage further research on temple paintings in the Kingdom. But for now, there are no plans to further investigate or decipher the mysterious icons at the world’s largest religious monument.

“We have no initiative yet to preserve or restore the paintings,” said Sokrithy, Apsara Authority’s deputy director. “But most people who come to Angkor Wat are looking for the reliefs and the architecture, so the paintings, which are mostly in the far corridors, aren’t facing any harm. But who knows, maybe soon people will be coming to try to hunt out the traces of paint.”