Alexander Borodai, prime minister of the self-declared Donetsk People's Republic (DPR), described evidence that showed otherwise as "fake".
However, in a separate interview a rebel military commander said he was aware rebel fighters had the weapon.
All 298 people on MH17 died when it crashed in east Ukraine last week.
Ukrainian pro-Russian rebels have been widely accused of shooting the plane down. Officials in Kiev said the rebels also shot down two Ukrainian military aircraft on Wednesday.
The Netherlands, where most of the victims were from, received the first bodies in a ceremony on Wednesday.
More bodies are expected to arrive on Thursday.
'Horror movie'
Speaking to the BBC's Gabriel Gatehouse in Donetsk, Mr Borodai rejected accusations that his men neglected crash victims' bodies.
He also categorically denied the presence of the Russian-made SA-11 Buk missile system in the crash area. Western intelligence officials say this was the weapon used to shot down the aircraft.
Out of media player. Press enter to return or tab to continue.
"Nations united in grief": Annita McVeigh reports on the return of the dead to the Netherlands
"No, we didn't get a Buk. There were no Buks in the area" he told the BBC's Gabriel Gatehouse.
He initially denied knowledge of photographs allegedly showing the presence of a Buk launcher in the nearby town of Snezhnoe, before saying that such photographs were fake.
Mr Borodai's comments came as Alexander Khodakovsky, commander of the rebel Vostok (East) battalion, said he was aware that a Buk launcher had been on its way from the neighbouring region of Luhansk to Snezhnoe.
"That Buk I know about. I heard about it. I think they [local rebels] sent it back... They probably sent it back in order to remove proof of its presence," he said in an interview with Reuters news agency.
更多英语新闻
