A top rebel commander in eastern Ukraine has reportedly said that the armed separatist movement had control of a Buk missile system, which Kiev and western countries say was used to shoot down a Malaysia Airlines plane last week.

Alexander Khodakovsky, who leads the Vostok battalion – one of the main rebel formations – said the rebels may have received the Buk from Russia, in the first such admission by a senior separatist.

"That Buk I know about. I heard about it. I think they sent it back. Because I found out about it at exactly the moment that I found out that this tragedy had taken place. They probably sent it back in order to remove proof of its presence," Khodakovsky told Reuters.

Russian news agencies later said people close to Khodakovsky denied he made the admissions. Khodakovsky himself told Life News, a Russian news agency with links to Moscow's security services, that he was misquoted and had merely discussed "possible versions" with Reuters. Khodakovsky said the rebels "do not have and have never had" a Buk.

As two further Ukrainian fighter jets were shot down, apparently by missiles fired from within Russia, Khodakovsky appeared to imply that MH17 was indeed downed by a missile from the Buk, assuming the interview with Reuters is confirmed. He blamed Ukrainian authorities, however, for allowing civilian jets to fly over its airspace when the rebels had such capabilities.

"The question is this: Ukraine received timely evidence the volunteers have this technology, through the fault of Russia," he said. "It not only did nothing to protect security, but provoked the use of this type of weapon against a plane that was flying with peaceful civilians."

Other leaders have repeatedly denied the rebels had a Buk, despite photographic and video evidence of one in the area of the crash last Thursday. There are rivalries and hatred between many of the rebel formations and Khodakovsky is believed to be out of favour with Igor Strelkov, the main commander of the Donetsk rebels.

However, his apparent admission about the Buk chimes with evidence on the ground. This week the Guardian also spoke to witnesses who said they saw a missile-launching system that looked like a Buk drive through Torez, near the crash site, last Thursday, a few hours before the plane was downed.

Khodakovsky said he did not know where the missile system had come from but it may have come from Russia. He added the separatists had seized several Buk systems from Ukrainian bases, but none of them were operational.

"I'm not going to say Russia gave these things or didn't give them," he said, according to Reuters. "Russia could have offered this Buk under some entirely local initiative. I want a Buk, and if someone offered me one, I wouldn't turn it down. But I wouldn't use it against something that did not threaten me. I would use it only in circumstances when there was an air attack on my positions, to protect people's lives."

The apparent admission came as the first bodies arrived in the Netherlands, after a long journey from Torez by train to Kharkiv, and then by plane to the Netherlands. Separatists said they loaded 282 bodies on to the train, but Dutch experts suggested the number actually handed over could be much lower. Monitors at the crash site say there are still human remains lying on the ground.

So far, only monitors from the Organisation for Security and Cooperation in Europe (OSCE) have visited the site, but in purely reporting function rather than any investigative role.

They were accompanied once by a three-man Dutch forensic team who monitored the transfer of bodies to the train but did not investigate the causes of the crash, and for the past two days by a small Malaysian delegation. There is still no security cordon around the site. The Dutch have taken the leading role in the international investigation, with the Dutch safety board taking charge of the team. On Wednesday, they said unfettered access to the crash site was crucial.

Spokesman Tjibbe Joustra told the Associated Press that around 25 investigators have arrived in Kiev and are analysing information from the crash site, including photographs, satellite images and radar information. However, they have not yet visited the site.

"We haven't yet got guarantees about security for our way of working," said Joustra. "If we go we have to be able to move freely. We hope to be able to get to the site soon."

It is unclear what they are waiting for. The rebels have said they are happy for any investigators to arrive and work at the site, and while the area is unquestionably dangerous given the ongoing military action in the vicinity, it is unlikely to become safer any time soon.

OSCE spokesperson Michael Bociurkiw said his team would do the best they can. "There has been a lot of talk about why there have been so few experts … We again feel that the work that remains to be done should be done by those far better qualified than us, yet in their absence we will continue to do the basic monitoring that we can."

The Dutch safety board also said that early examination of the black boxes from MH17, which have been sent to Britain for decoding, showed no evidence they had been tampered with. The black boxes were handed to a Malaysian delegation earlier this week in Donetsk by the region's self-declared prime minister, Alexander Borodai, who used the occasion to accuse Ukrainian forces of downing the plane.

Also on Wednesday, Ukraine's security council said two of its Su-25 military jets had been shot down, and added that the planes could have been brought down by missiles fired from inside Russia's borders.

"Two of our jets were hit at an altitude of 5,200 metres. According to preliminary information, the missiles were launched from the territory of the Russian Federation," the council said in a statement.

The planes were flying far lower than the altitude above 10,000 metres where MH17 was when it was shot down, but still out of usual range for the Manpad shoulder-launched missiles the rebels are known to possess.

Footage purporting to be from the crash scene of one of the planes showed a group of rebels arriving to find the burning wreckage.

One of them said the pilot had parachuted out before the plane crashed and the men set off to search for him.

• A subheading on this article was amended on 28 July 2014 to more

accurately reflect the content of the article.