The clue starts at the Prometheus cast and crew page at 
IMDB which has been updated with an entry for 
Adam Sculthorp, who is now listed as 
"stereographer: Jordan, Iceland & vex units".
A further search leads to cinematography specialists 
4K London, who's team consists of one 
Mary Lobb who is listed as wrangler for Prometheus on IMDB.
According to her 
profile on the 4K website:
"Mary acted as  Data Wrangler for the entire main unit shoot of Ridley Scotts  'Prometheus', based predominantly at Pinewood Studios, but also  including location work in Jordan and Iceland."
Also, the 
Royal Film Commission of Jordan has listed Prometheus on their 
list of films for 2011. According to their newsletter from 
June 2011, the filming took place in May 2011.
Originally the production crew were scheduled to shoot certain scenes in 
Morocco last  year, but apparently the producers decided last minute to move to  another location due to the civil unrest in the area at the time.
As to what was actually shot in Jordan will remain a mystery for the  time being. There have been rumors circulating that the Prometheus story  starts with an excavation on Earth revealing ancient alien artefacts  which leads the story towards space. Could Jordan be the filming  location for these excavations?
Other movies filmed on location in Jordan include
 Lawrence of Arabia, 
Indiana Jones and the Last Crusade, 
Hurt Locker and 
Transformers: Revenge of the Fallen.