It yielded reports of apparitions, phantom footsteps, unexplained cold spots and unseen hands.
But Prof Wiseman does not believe the experiences were paranormal. He said environmental and psychological factors were responsible for the hauntings.
Mary King's Close is a warren of underground streets sealed off from the outside world more than two centuries ago.
It became entombed when Edinburgh's Royal Exchange - now the City Chambers - was built in 1753.
The top floors of the houses were demolished and the lower floors incorporated into its foundations.
The rooms of many houses still exist, and according to some reports, so do a number of their former residents.
Prof Wisemen sent groups of volunteers to four locations, without telling them that only two sites had a strong reputation for being haunted.
The aim was to compare reports from the different sites.
About 70% of those visiting the "haunted" locations reported unusual phenomena.
In contrast, only 48% of people exploring the locations not reputed to be haunted had spooky experiences.
At the "most haunted" site, where a sinister figure in black has repeatedly been seen, more than 80% of the volunteers reported something strange happening.
"There was a massive difference between the locations," said the professor from the University of Hertfordshire.
"Sometimes people just felt very cold, but there were some quite extreme experiences - feelings of being watched, being touched and having clothing pulled, apparitions of people and animals, and footsteps. I was really surprised at the extent of the experiences."
Experiments by the researchers showed that the two "haunted" locations were significantly less humid than the other sites.
This can generate a feeling of coldness, said Prof Wiseman.
There was also evidence of "infrasound" - low frequency sound waves which are too deep for the human ear to pick up, but are known to produce feelings of unease.
In the most haunted site there was a continuous infrasound rumble, which may have been due to traffic overhead.
A psychological test also found that people rated photos of the haunted locations as significantly more "ghostly" and sinister than the other sites, without knowing their reputation.
This suggested that subtle visual features, such as shape, lighting, or the presence of doorways, may be eliciting a sense of fear.
Prof Wiseman said: "It could be that the ghosts were down there, but I think the explanation is primarily psychological."