The 32-year-old Spaniard is described as being in a "critical but stable" condition after undergoing considerable overnight surgery at Addenbrooke's Hospital in Cambridge.
Team principal John Booth said: "Maria emerged from theatre at Addenbrooke's Hospital this morning after a lengthy operation to address the serious head and facial injuries she received in the accident.
"We are grateful for the medical attention that Maria has been receiving and her family would like to thank the neurological and plastics surgical teams.
"However, it is with great sadness I must report that, due to the injuries she sustained, Maria has lost her right eye."
De Villota, who joined Marussia as test driver in March, was taking part in her first test for the team, a straight-line aero at the old Second World War site.
De Villota had just completed her initial installation run when her car ran into the tailgate of a support truck at around 20-30mph, which was at such a height to inflict the head trauma.
Initially her injuries were described as "life-threatening" by an ambulance service spokesman, only for more encouraging statements to follow later on as De Villota was reported to be conscious.
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Marussia have now confirmed, however, surgery began on Tuesday afternoon, with De Villota in theatre until Wednesday morning.
Booth added: "Maria's care and the wellbeing of her family remain our priority at this time. Her family are at the hospital and we are doing everything possible to support them.
"We ask for everyone's patience and understanding with regard to updates on Maria's condition.
"We will provide further information when it is appropriate to do so and with consideration for her family.
"In the meantime, we would all like to take this opportunity to praise the emergency services at Duxford Airfield, who were on stand-by yesterday [Tuesday], as is usual procedure for a Formula One test.
"Finally, we have been overwhelmed by messages of support for Maria, her family and the team and we would like to express our sincere gratitude for those."
Early theories behind the accident have suggested the anti-stall mechanism on the car kicked in as she approached a makeshift pit area, suddenly propelling her into the truck.
Booth has confirmed investigations into the accident are ongoing, adding: "We have embarked on a very comprehensive analysis of what happened and this work continues for the moment."