People living near the scene of the shooting, which happened on a slip road near junction 24 at around 6pm on Monday, described the frightening sight of officers “swarming” around a group of vehicles after the incident.
At the scene, a silver Audi with bullet holes in its windscreen was surrounded by other vehicles at the bottom of the off-slip of the westbound carriageway.
West Yorkshire Police said the operation was not terror-related and that a car had also been stopped in the Chain Bar area of Bradford at around the same time.
Shahnaz Malik’s house is the closest to the scene and overlooks the slip road from the village of Ainley Top.
The 54-year-old said she was not aware straight away that there had been a shooting, first thinking it was a major accident.
She said: “We do have accidents and we hear sirens. It just seems like there were too many last night.”
Ms Malik said that once she realised something out of the ordinary was under way, she looked over her back fence and saw large numbers of police vehicles and officers.
“There was like a swarm,” she said. “There was a lot. It was dark as well.”
She said: “It was surreal. It was like time had stood still, so many police buzzing around.
“It all happened so quickly. I was just stood there freezing cold.”
Asked why she had looked out in the first place, she said: “It just didn’t feel right. I thought it must be a major accident.
“I didn’t know what I was looking at, to be honest. It was like time had stood still but, obviously, all this movement was going on. I didn’t even occur to me there might have been a shooting.”
Ms Malik said Ainley Top was a tight-knit community and the shooting has shocked people living in the area.
“It’s quite frightening. It’s a little village and we all sort of know who’s who.”
She added: “It’s absolutely horrendous. This is a major incident. Somebody has been shot and killed. You hear about this on the news.”
Five people were arrested across the two vehicle stops - three in Huddersfield and two in Bradford.
Several of those arrested needed hospital treatment for injuries “not related to firearm discharge” but no police officers were hurt, a force spokesman said.
The dead man’s identity has not been released and police are yet to confirm any further details about the operation.
The force said it had informed the Independent Police Complaints Commission and was “fully co-operating” with the watchdog’s investigators.
The eastbound carriageway of the M62 is open at junction 24 but all other sliproads remain closed while the investigation continues.
A police spokesman said: “During a pre-planned policing operation near to the M62 in Huddersfield a police firearm was discharged and a man has died.
“An immediate referral has been made to the Independent Police Complaints Commission who are in attendance in West Yorkshire and West Yorkshire Police are fully co-operating with their investigation.”
Witnesses reported seeing “five or six” police cars, a Mercedes E Class and a Jaguar at the scene.
Local councillor Gemma Wilson said she was driving home from the cinema when she saw at least five or six police cars go past.
She said: “The police cars were used as a barricade to stop people getting on to the motorway.
“The initial speculation was it was a crash and I assumed it was some sort of massive pile-up.”
An IPCC spokesman said: “An IPCC independent investigation is under way following the death of a man during a pre -planned police incident in Huddersfield. The IPCC understands that the man was shot by a West Yorkshire Police firearms officer shortly after 6pm on Monday 2 January close to Junction 24 of the M62 motorway.
“IPCC investigators remain at the scene and are attending post-incident procedures in order to gather evidence during the early stages of this investigation. The man’s family has been informed.”