Deputy Commissioner Sir Stephen House said the health checks required after spitting caused huge stress to officers.
Speaking at the London Assembly’s police and crime committee, he said: “If you’re spat at you have to go through a check to make sure you’re not going to be subject to some kind of viral infection.
“That treatment if it has to be carried out can last weeks and sometimes months and creates a huge amount of anxiety in the officers.
“I’ve spoken to many officers who’ve said quite frankly if it was a choice between being spat at in the face and punched they’d rather be punched – because although it might hurt more it’s immediate and you know what you’re dealing with.”
The Deputy Commissioner’s comments came in the wake of assaults on police at Notting Hill Carnival – which included officers being spat at in the face.
There were 33 assaults on police during the August bank holiday festival, down five from the previous year.
The Deputy Commissioner said it was the “duty” of police to cover the event despite the prospect of violence, but that “any assault on police is unacceptable”.
Conservative assembly member Susan Hall said spitting at officers was “absolutely vile”.
Ms Hall said she was concerned that after she had “screamed and ranted at the wretched Mayor” to convince him to give spit hoods to all London police, officers on the front line were still unprotected.
Spit guards were promised by Met Commissioner Cressida Dick in February, but have yet to be rolled out, she said.
Ms Hall said she was worried about the safety of police at the carnival, and questioned whether the event should be moved to a different location in future, to make it easier to police.
But Labour’s Florence Eshalomi said violence at the carnival should not overshadow the broader benefits of the event.
She said: “Carnival is a cultural event – it’s not an event where the police need to be forceful, it’s not a demonstration, it’s not a protest.
“It’s a range of people coming together to celebrate everything that’s good about London and the Caribbean community.”