Elite funding agency UK Sport has told British Cycling's board it has "serious concerns" about its handling of allegations against ex-technical director Shane Sutton and has still not received key information about the case.

Last April, former Great Britain rider Jess Varnish claimed Sutton used sexist language towards her, and in October an internal British Cycling investigation led by board member Alex Russell upheld that complaint.

But six weeks later, when the minutes from a British Cycling board meeting were leaked, it emerged Sutton had only been found guilty of one of nine charges.

According to those minutes, the board believed "on the balance of probabilities" that Sutton did use the word "bitches" during training but did not tell Varnish to "go and have a baby", use the "c word", make negative remarks about her weight or discriminate against female riders.

This set of decisions left both Sutton, who has repeatedly claimed his innocence, and Varnish, who was dropped from the British team four months before the Rio Olympics, threatening legal action.

But a Freedom of Information Act request by Press Association has now revealed UK Sport, which has granted British Cycling £26m for its preparations for Tokyo 2020, also has strong misgivings about the board's decision.

On December 14, UK Sport chief executive Liz Nicholl emailed British Cycling's then-chairman and president Bob Howden to follow up on a conversation they had the day before, with UK Sport chairman Rod Carr copied in on the email.

Nicholl writes that she wanted Howden to explain how the board reached its decision on Sutton and restates her request for "copies of the policy applied".

She continued: "I also questioned why UK Sport had not been fully informed of the facts. It was a surprise to hear of the board's involvement of anything other than ensuring due process and handling reputation management, and a shock to hear it revealed in the media that 8/9 of the complaints considered by the internal review (had) not been upheld."

Thanking Howden, who stood down as chairman in February but remains British Cycling's president, for being "so open" in their conversation the day before, Nicholl wrote she has "serious concerns about your process, not least that it was the board that made the findings of fact about the allegations, not the person (Russell) who had directly heard the evidence".

Nicholl has expressed her concerns on behalf of UK Sport (Getty)

Nicholl then criticised Howden for making the "incorrect assumption" UK Sport's board would have been told about Russell's investigation via the separate and much wider independent review looking at the "climate and culture" of the GB cycling team.

Russell's full report, including her personal recommendations, has been shared with the independent review referred to by Nicholl.

The UK Sport boss concludes the first half of email on her "concerns about the judgement calls that appear to be being made at chair and board level" by asking Howden "to ensure" she receives a copy of Russell's report and the board's minutes, which have been redacted on the British Cycling website.

Sutton resigned from British Cycling while the investigation was carried out (Getty)

This request, however, has not been met, with British Cycling telling UK Sport the Varnish case is an internal "grievance" and Russell guaranteed anonymity to those who spoke to her.

The independent review has been conducted by a five-strong panel led by British Rowing chair Annamarie Phelps and its final and much-anticipated report is imminent.

A draft report completed before Christmas, however, was leaked to the Daily Mail earlier this month and its preliminary findings were scathing of British Cycling. It accused the board, all of whom are still in place, of "sanitising" Russell's report and even "reversing" her findings.

This draft report, which has been the subject of intense legal wrangling over the last three months, said the board ignored Russell because of Sutton's success as a coach and Varnish was dropped as "an act of retribution" for criticising coaches after failing to qualify for Rio in the women's team sprint.

Varnish does not believe Sutton should be allowed to work in cycling again (Getty)

The report, which was written by top sports lawyer John Mehrzad, concluded: "The actions of the British Cycling board in that regard are shocking and inexcusable. They also call into serious question whether the composition of the British Cycling board is fit to govern a national sporting body."

Since then, however, Howden has been replaced as chairman by former motor industry executive Jonathan Browning, a board member since 2015, and the governing body has appointed a new chief executive and performance director. It has also released a 39-point "action plan" to address the athlete-welfare issues raised by the Varnish affair and flagged up in the independent review.

Nicholl and UK Sport have been publicly supportive of these steps, as has grassroots funding agency Sport England, but Press Association reports that there are growing calls for a more radical overhaul at British Cycling, with some senior voices suggesting Browning should step down, too, given his involvement over the last two years.

Nicholl closes her email to Howden by saying she wants "to help British Cycling be even better, not only in terms of medal success, as we know you are world-class in that respect, but also in terms of leadership, management, engagement, communication and duty of care".

She wrote: "Bob, never doubt we want you to succeed, but when we are investing millions of public funding in an organisation, a significant level of accountability and responsibility rests with its leadership and management."

In response to why British Cycling has still not shared its internal investigation into Varnish's claims with UK Sport, a spokesperson at the governing body said "interviewees provided information on the understanding it would be confidential and shared only with the British Cycling board and with the independent review panel".

British Cycling has seen its reputation tarnished be recent incidents (Getty)

Emails seen by Press Association confirm Russell and Phelps were in regular contact last year as they conducted their separate investigations and Russell's report was shared in full with the independent review in October.

"British Cycling takes its responsibilities very seriously to ensure the organisation is managed with integrity, excellence and due process," the British Cycling spokesperson added.

"That is one of the premises of our action plan which has been developed in response to the recommendations of the independent review, which we are moving quickly to implement thoroughly as part of our ambition to become a world class governing body."