The police spokesman said that there were no plans to remove the tweet.
However, ground operations director for the NPAS, superintendent Richard Watson later admitted that the picture was "inappropriate" and would be deleted.
"We are aware of the tweet and, as far as we are aware, it does not breach any data protection legislation," he said. "We will be speaking to the person who posted the tweet."
The ICO later confirmed they were investigating the incident, explaining that "processing personal data and disclosing images of this nature without a justifiable policing purpose" could amount to a breach of the Data Protection Act.
McIntyre was photographed outside the Global Radio offices in Leicester Square at around 8am on Wednesday morning.
The comedian's publicist, Alison Peters, who is also featured in the CCTV image carrying a large handbag, confirmed the picture was of her and McIntyre, calling it "crazy".
Other Twitter users complained about the tweet.
Emma Carr, director of Big Brother Watch, an organisation which campaigns against excessive state surveillance, said: "At best posting this image was a complete waste of time.
"At worst, NPAS seem to have had complete disregard for the surveillance and data protection laws that are there to protect our privacy.
"CCTV is there to keep our streets safe, not to intrude on the privacy of celebrities."
Police aircrafts carry a variety of hand-held digital cameras, capable of taking high-resolution images to be used for evidence or to assist officers in planning and executing operations. They can also stream live footage to command bases.
Human rights campaigner Peter Tatchell said it was "highly inappropriate" for police to tweet a picture of McIntyre "going about his private business".
He went on: "I can't see the justification of such intrusion.
"It's quite right for police services to tweet messages about criminal investigations and appeals for public assistance but this photo seems just a laugh and celebrity gossip. It doesn't really fit a theory of police service."
Rachel Robinson, policy officer of human rights organisation Liberty, added: "NPAS is getting a reputation for irresponsible tweeting and, with public concern around the misuse of state surveillance growing, this latest example suggests a blase attitude to our privacy.
"This doesn't bode well for those of us concerned about police use of new surveillance technology such as drones. How confident can we really be that our privacy is being taken seriously?"
An ICO spokesperson said: "Police forces like all other organisations must comply with the Data Protection Act.
"The police especially must ensure that they have legitimate grounds for processing personal data and disclosing images of this nature without a justifiable policing purpose could potentially breach the Data Protection Act.
"We will follow this up with the force concerned."
The comedian was due to perform in Ipswich ahead of his Happy And Glorious UK and Ireland tour on Wednesday night. His spokesman said that police "should be spending their time more wisely".
