While acknowledging police "got things badly wrong," Stephen House told BBC that the "massive changes" to policing in Scotland weren't the cause.
"This has been a horrible tragedy," he said. "I feel it, we all feel it very badly. But it should not detract from the fact we're changing the system because we believe it will produce a better system for the public."
Bell was found last Wednesday beside her dead boyfriend, John Yuill, 28, in a car that had slid down an embankment on the M9 highway near the city of Stirling in central Scotland.
Their Renault Clio had gone off the road on Sunday morning. A call was made to Police Scotland, but there was no response. A second call on Wednesday sent police to the scene of the accident.
Bell was taken to hospital in Glasgow, where she died Sunday, one week after the accident.
In an earlier statement, House said the first call to police from "a member of the public" wasn't entered into police systems properly.
"All callers to 101 receive an electronic options menu," House's statement said. "This call was answered within six seconds following that message by an experienced officer and the relevant details were given by the caller.
"For reasons yet to be established, this call was not entered onto our police systems and not actioned out to operational teams in the Stirling area to respond and trace the vehicle."
House's statement was published by the Guardian.
On Sunday, the Scottish government announced a formal investigation into the handling of police calls.
House tweeted that he welcomed the probe.
The dead woman's family remains overwhelmed by the tragedy.
"A huge error by a senior officer has absolutely devastated us ... it feels like we have had our hearts ripped out. Any time I see her my heart sinks to the bottom of my stomach and it's not getting easier," Lamara Bell's father, Martin Bell, said in a Facebook post.
House said earlier this year that he is likely to leave his job in September 2016 when his contract expires, the BBC reported.