Prince William was "left concerned" after he and Kate Middleton were "aggressively" pursued by paparazzi, officials have said.
Prince William and Kate Middleton were chased in their car
The prince and Miss Middleton were in a car during the incident, Clarence House said on Friday. The pictures were published in London's Evening Standard.
William's spokesman said the events were "incomprehensible" at this time.
This week saw the start of an inquest into the death of William's mother, Diana, Princess of Wales.
Her car crashed in Paris in 1997 as she was being followed by photographers.
The couple, who have rekindled their relationship after splitting up briefly in April, were leaving the Boujis nightclub in London during the early hours of the morning when the incident took place.
The Daily Mail, sister newspaper of the Evening Standard, has withdrawn plans to print the photographs on its front page. It has substituted a paparazzi picture with an earlier shot of the couple watching rugby.
The Daily Mirror said it will not use the images.
Paddy Harverson, the prince's spokesman, said: "Prince William was concerned by the threatening behaviour of the paparazzi in London last night.
"Having already been photographed leaving the club, he and Kate Middleton were then pursued in his car by photographers on motorcycles, in vehicles and on foot.
"The aggressive pursuit was potentially dangerous and worrying for them. It seems incomprehensible, particularly at this time, that this behaviour is still going on."
Mr Harverson said the matter has been raised with the Press Complaints Commission.
'Safety of individuals'
In a statement the PCC said that while freelance photographers are not directly regulated by the organisation, editors must not publish photographs which are taken through harassment.
It said: "It can of course be difficult for editors to establish the exact circumstances in which a photograph is taken.
"But it is of the utmost importance not to use photographs which have been taken in a manner that may have compromised the safety of individuals, which may include pursuit in vehicles."
Alessandro Copetti, who took the picture published in the Evening Standard, said the prince's car was only followed when it returned to the club shortly after leaving.
"The car stood there for a few seconds then departed, then left," he told BBC Radio Five Live.
"Then the car disappeared, nobody chased, nobody followed. Then four minutes or five minutes later the car comes back and drives slowly in front of about the same amount of photographers so some people made the wrong choice to start chasing."
The publicist Max Clifford told BBC News 24 it would have been better for the couple to have avoided confrontation by posing for the photographers.
"If this is the first time they've been together for months, you know there's going to be considerable interest," he said.
"They know that they're going to be photographed when they come out. So, they stand for five minutes and pose for pictures.
"Everybody's got their pictures - nice pictures, relaxed pictures - they go away, because they don't need to chase them," Mr Clifford added.
The prince and Miss Middleton met while at St Andrews University.
The inquest into the deaths of Princess Diana and her companion Dodi Al Fayed began on Tuesday at the High Court.
The jury has heard how several photographers pursued the princess's Mercedes prior to the fatal crash in the Pont de l'Alma tunnel, which killed her, Mr Al Fayed and their driver Henri Paul.