Van der Mark crashed his BMW M1000RR at Turn 10 at the beginning of the 45-minute session in Portugal, forcing the race control to bring out the red flag.
The Dutch rider was initially taken to the circuit medical centre as per routine before being transported to Hospital de Sao Jose in Lisbon for further checks.
It was discovered that van der Mark had fractured the neck femur on his right hip, leaving him unfit for the remainder of the race weekend.
The accident compounds an injury-ridden start to the 2022 season for van der Mark, who was already forced to miss the Aragon season opener after breaking his leg in a training incident earlier in the year.
Van der Mark returned to action at the second round of the season in Assen, his home event, but admitted that he wasn’t feeling 100 percent on the bike.
BMW will not be able to replace the 29-year-old in Estoril, leaving Scott Redding as the sole representative for the outfit’s factory team in the third round of the season. The British rider finished 11th-quickest in first practice, four places behind Eugene Laverty on the satellite Bonovo MGM BMW.
Van der Mark was previously replaced by IDM champion Ilya Mikhalchik when he couldn’t take part in the Aragon opener.
UPDATE: Ahead of qualifying on Saturday, BMW revealed that van der Mark had undergone surgery on his fractured neck femur on Friday night, reporting that the operation was a success.
The Dutchman now faces a race against time to be fit for the next round at Misano on June 11-12, although the following round at Donington Park in mid-July may be a more realistic target for a return.