The bodies of three spectators killed when a rally car ploughed into them were being removed by police on Sunday as questions were raised about safety procedures.

Iain John Provan, 64, Elizabeth Allan, 63, and John Leonard Stern, 71, all from greater Glasgow, died during the Jim Clark Rally on Saturday in the Scottish Borders. Six others were injured, including two critically, after two accidents within two hours on the closed-road course in the Duns and Kelso areas.

As a police investigation began, the organisers of the rally extended their condolences and sympathy to the families and friends of those affected. They said the event was "as safe as possible".

Alan Johnstone, media manager for the rally, said: "This is the first fatality we have had and it's been one very bad day." He told ITV news: "We try our level, level best to get it as safe as possible. You'll never get it 100% by its very nature."

The deaths occurred in the second crash at about 4pm at Little Swinton, near Coldstream, when a rally car came off the road and ploughed into spectators.

One witness said the spectators should not have been allowed to stand in that position. Teacher Colin Gracey, who saw the accident, said in previous years the area had been taped off at least 30 metres into the field, but on this occasion the tape was nearer. He told Sky News that there was also no steward's car parked near the area, as there had been in previous years.

Gracey said a safety car passed through the area ahead of the rally to tell people to stand at a safe distance: "A marshall car came through before the stage started and told people to move away from the area. I think people moved but came back."

Gracey added: "There were at least a dozen people standing there [in the crash area] and when it happened I thought, my God. It was horrendous, I've never seen anything like it in my life.

"The tape marking the course was next to the hedge where normally the tape is 30 metres either side of the road into the field and effectively no one is allowed down there unless you're a steward. We wouldn't even stand in the field. We always go a bit further up the road which is safer."

Two hours before the crash, another car in the rally left the road and hit five people – one women and four men – near Crosshall Farm on the Eccles stage of the competition. Three of the men were taken to Borders General hospital, with one later moved to an intensive car unit in Edinburgh. The remaining two were treated for minor injuries. It is understood the rally crew of the two cars were unhurt.

The rally, named after Scottish Formula One driver Jim Clark, who grew up in the area and who died in a motor racing accident in Germany in 1968, was due to finish on Sunday but was abandoned after the fatal crash.

Superintendent Phil O'Kane, of Police Scotland, said officers were working to "forensically and sympathetically removed the deceased from the scene". He said he thought the rally organising committee "would have considered it was safe to move on to the next rally stage" after the first accident.

"It's the nature of the event, a rally on open roads that the public have access to. Although safety barriers are put in place, there are not stewarding positions along the whole route. It's a high-energy and a high-adrenaline sport and people want to take the best positions," he said.

Spectator Tony Cowan told the BBC: "It was just one car which lost control. It went sideways one way and then to the other side of the road and ploughed into four people.

"It was terrible, absolutely terrible. I ran to help but there was little I could do. The air ambulance arrived after about three quarters of an hour. There were police cars and ambulances. It was chaos, just chaos."

In a statement, rally organisers said they were in shock. They added: "Berwick and district motor club, Border Ecosse car club, and the governing body, the Motor Sports Association (MSA), are co-operating fully with the police investigation.

"As with any serious incident on a motor sport event, the MSA will conduct its own thorough inquiry once the police investigation is concluded."

Scotland's first minister, Alex Salmond, called the deaths "desperately sad and difficult news".

He added: "The Jim Clark Rally is a long-standing event of over 40 years. It is much loved in the borders and by the rally driving community who I know will share in our sadness at what is a black day for the borders and for Scotland."

Local MSP John Lamont said his "thoughts and prayers are with the victims and their families".

"I know the rally organisers place considerable emphasis on the safety of the spectators and drivers but, with any event of this nature, there will always be an element of risk." He said it was "appropriate that questions are asked and investigations are carried out to ensure that in the future nothing like this happens again".