Kevin Hurley, Surrey Police and Crime Commissioner, said he had considered seeking her dismissal before she took over the national policing role.
Concerns about public protection and child safeguarding in Surrey were down to a "failure of leadership", he said.
Mrs Owens said she underwent a "lengthy and thorough" NCA interview process.
The Home Office said she was an "exceptional" policing leader.
Last November, Mrs Owens, 47, saw off strong competition to be named director-general of the National Crime Agency - one of the most prestigious and highly paid roles in policing.
The NCA has responsibility for the Child Exploitation and Online Protection Centre - known as CEOP.
But in the months leading up to her appointment, Mrs Owens's record on child protection had been brought into question by Mr Hurley.
Highly critical inspection reports of the force had led Mr Hurley to declare that he had lost confidence in Mrs Owens and was considering starting the formal process - known as Section 38 - that could have led to her dismissal.
Criticisms included the Independent Police Complaints Commission (IPCC) finding failings in the way the Surrey force had handled the case of 14-year-old Breck Bednar, who was groomed online before being murdered.
Mr Hurley had previously been a supporter of his chief constable, extending her contract in 2012 and writing to Home Secretary Theresa May in 2014 to say she had had an "outstanding year".
But during the 12 months leading up to November 2015, all that had changed.
Emails and documents disclosed to BBC News under the Freedom of Information Act show that over this period, Mr Hurley's confidence in the chief constable's ability to deal with the problems ebbed away.
The minutes of a public protection scrutiny meeting on 3 September reveal the PCC's concerns about the force's handling of rape, domestic abuse and female genital mutilation cases - as well as child protection.
In September, Mr Hurley wrote a stinging 10-page letter to Mrs Owens saying he held her "personally responsible".
He accused her of blaming others for the "litany of failures", claiming it was "an example of moral cowardice".
He wrote: "You have failed to act decisively or speedily to address many areas of concern in relation to public protection."
Mrs Owens has told the BBC these comments were "ill-considered and inaccurate".
Mr Hurley delivered the letter to Mrs Owens at a meeting, during which she declared that she was applying for the NCA post.
At the same meeting, Mr Hurley revealed he had been considering starting the formal process that could lead to Mrs Owens being dismissed or having to resign from the force.
Mr Hurley then wrote to Sir Tom Winsor, the Chief Inspector of Constabulary for England and Wales, stating concerns that Surrey Police was "failing vulnerable children, rape and domestic violence victims" and asking for assistance.
Mrs Owens issued a detailed 19-page rebuttal of the PCC's accusations, saying her 26-year police record was "unblemished" and that she had taken "immediate and muscular" action in response to child protection concerns.
But in October, Mr Hurley wrote again to Sir Tom, saying: "I have lost confidence in the chief constable's ability to lead the necessary cultural changes and cannot be sure that, under her command, the threat, risk and harm of public protection-related issues will be properly addressed."
Mr Hurley has said he was not asked about Mrs Owens's suitability for the NCA position, and only found out about her new job by a message posted by a journalist on social media.
He said that had Mrs Owens not been appointed he would have started the formal dismissal process.
He told BBC Radio 4's Today programme: "It is a failure of leadership. The chief constable is the leader. She has let down the constables and sergeants, but more importantly she has let down our most vulnerable victims across the county."
The Inspectorate of Constabulary said it had briefed senior officials at the Home Office concerning the inspection work at Surrey, the "nature of the correspondence" from Mr Hurley and discussed the NCA appointment with them.
However, it is understood that another inspectorate report, which is due to be published in the coming weeks, is expected to conclude that the force lacks understanding of serious and organised crime groups in Surrey and "requires improvement" in the way it deals with the problem.
Mrs Owens said: "I was selected to my current role by the home secretary after a lengthy and thorough process and am now focused on leading the National Crime Agency in its fight to cut serious and organised crime."
The Home Office said Mrs Owens was "one of the exceptional policing leaders of her generation".
Officials pointed out that she went through a rigorous recruitment and selection process that included a "testing" panel interview. It said professional references and due diligence checks were also undertaken.
New National Crime Agency head Lynne Owens was appointed amid concerns about her performance as chief constable of Surrey Police, the BBC has learned.