Ms Munchetty was reprimanded over comments about racism and Donald Trump made during a July programme. The broadcaster has since reversed its decision to censure the presenter.
Following an assessment, Ofcom said that Naga Munchetty’s comments about racism and Donald Trump would not have breached its broadcasting rules.
The media regulator received 10 complaints related to the programme and the BBC’s decision to reprimand Ms Munchetty.
But in a series of letters sent to the regulator, David Jordan, a BBC executive, argued the watchdog did not have the jurisdiction to conduct the assessment. Ofcom said it was publishing the correspondence in the interests of transparency.
The media regulator said it had “serious concerns” over the BBC’s complaints process, after examining the presenter’s remarks.
“Due impartiality rules are vital for maintaining high levels of trust in broadcast news,” said Kevin Bakhurst, Ofcom’s group director for content and media policy.
“We took into account the format of the BBC Breakfast programme and the nature of the presenters’ exchange.
“Our assessment is that it would not breach our broadcasting rules and does not warrant investigation.
“More widely, we have serious concerns around the transparency of the BBC’s complaints process, which must command the confidence of the public.
“We’ll be requiring the BBC to be more transparent about its processes and compliance findings as a matter of urgency.”
The Independent understands the broadcaster’s complaints framework has previously been approved by Ofcom.
Tony Hall, the BBC’s director general, reversed the decision to reprimand Ms Munchetty last week.
But Ofcom continued to carry out its assessment.
Published correspondence reveals that David Jordan argued Ofcom did not have the authority to investigate the scandal, following the reversal.
“We continue to disagree with Ofcom’s approach,” Mr Jordan said in a letter sent on 4 October.
“We remain of the view that there is no proper basis for Ofcom’s proposed action.
“I am disappointed, therefore, that Ofcom is assessing a broadcast with a view potentially to undertaking an investigation for which it has no clear jurisdiction, rather than handling the complaints it has received about the programme in the normal way.”
In July, Ms Munchetty addressed Donald Trump’s Twitter diatribe against four congresswomen of colour, in which he told them to “go back and help fix the totally broken and crime-infested places from which they came”.
“Every time I’ve been told as a woman of colour to ‘go home’, to ‘go back to where I’ve come from’, that was embedded in racism,” the presenter said.
“Now, I’m not accusing anyone of anything here, but you know what certain phrases mean.
“I can imagine lots of people in this country will be feeling absolutely furious that a man in that position feels it’s okay to skirt the lines with using language like that.”
Questioned further by Dan Walker, her co-host, Ms Munchetty said she was “absolutely furious a man in that position thinks it’s OK to skirt the lines by using language like that”.
The remarks prompted a complaint, which argued that her comments breached the broadcaster’s impartiality rules.
The broadcaster partially upheld the complaint, before Mr Hall’s subsequent intervention.
Ms Munchetty has not commented on the BBC or Ofcom’s decisions.
“We note Ofcom’s finding and the fact they agree with the director general’s decision,” a BBC spokesperson said.