Video recorded in Islington, London, shows two officers holding a handcuffed suspect, who is black, on the pavement.
A second officer has been removed from operational duty following the arrest on Thursday evening.
Deputy Met Police commissioner Sir Steve House said the footage was "extremely disturbing" and had been referred to the police watchdog.
The force confirmed it had charged a 45-year-old man with possession of a knife in a public place.
Marcus Coutain, of Islington, is due to appear in custody at Highbury Corner Magistrates' Court on Saturday.
'Get off my neck'
In the footage, shared with the BBC, one of the officers appears to be using his knee to control the suspect and has his hand on the man's head.The man on the ground, who is in handcuffs, repeatedly shouts: "Get off my neck."
He is eventually released from the ground and continues to talk to officers after they sit him up.
Several police cars arrive at the scene after the arresting officers are confronted by onlookers.
An eye witness told the BBC: "I was worried he was going to get executed. That's just how George Floyd got killed.
"If not for the crowds filming the police they could have suffocated him or broken his neck.
"He was on the floor and in handcuffs, what's the reason for a kneeling on his neck?"
Technique 'not taught'
Sir Steve said: "The video footage that I have seen today and is circulating on social media is extremely disturbing."Some of the techniques used cause me great concern - they are not taught in police training.
"One officer has been suspended and another officer has been removed from operational duty, but not suspended at this time. This decision will be kept under review."
The man had since been seen by a doctor, Scotland Yard said. It has also referred the arrest to the Independent Office for Police Conduct (IOPC).
BBC home affairs correspondent Danny Shaw said Sir Steve's comments were highly unusual both in tone and content, particularly because the force had seen police body-worn footage which has not been made publicly available.
He added that the former Police Scotland chief constable had complained earlier this week that some officers were being unfairly targeted because of social media clips which did not show the full context of situations.
London Mayor Sadiq Khan said: "I'm deeply concerned about this distressing incident and we have raised this with senior officers at the Met Police as a matter of urgency.
"I welcome the fact the incident has been reviewed quickly by the Met and it's right that they have referred it to the IOPC."
The IOPC said it would conduct an independent investigation, according to the Met.
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