Senior figures at the funding body UK Sport told its in-house governance unit to “go easy” on British Cycling because “that’s where the medals come from”, more than two years before Jess Varnish made public allegations of bullying and sexism, the Guardian has been told.

Other UK Sport insiders have also come forward to tell of their deepening unease about a culture where the zeal to beat the London 2012 medal haul at the Rio Olympics dominated everything and led to less-strict governance checks than they felt were required.

As one senior source told the Guardian: “With cycling, the UK Sport governance team felt they couldn’t ever go firm on them on any issue because they would come under pressure from the performance guys if they started poking around too much. No one wanted to disrupt the medal factory. It had the status of a special sport.”

The allegations will ramp up the pressure on UK Sport, which will invest £345m in lottery and taxpayer funding in the run up to Tokyo 2020, over its “no compromise” approach and whether it should have done more to spot the problems laid bare in a damning independent report that was leaked last week.

However in a statement UK Sport said: “We completely refute the allegation that senior figures in our performance team did not want anything to get in the way of the people deemed to be delivering the medals. This is simply not the case. It is widely known within the high performance system that the Mission process includes a focus on athletes, system and climate.”

Conversations with current and past employees of UK Sport and the English Institute of Sport paint a picture where the performance department led by the director, Simon Timson, and the deputy director, Chelsea Warr, ruled the roost in the run-up to Rio. Timson, in particular, was obsessed with beating the London 2012 tally of 65 Olympic and 120 Paralympic medals and would go around UK Sport’s office saying “66/121” like a mantra.

But that desire for medals and resources is said to have led to Timson butting heads against the governance department led by David Cole, UK Sport’s chief operating officer, who felt his focus on improving the scrutiny of – and leadership capability within – national governing bodies was afforded far lower priority and resource than the pursuit of medals.

When the Guardian spoke to the Lawn Tennis Association, where Timson now works as performance director, it referred us to UK Sport, which said the notion that Cole and Timson were at loggerheads was “completely unfounded”.

The Guardian has also been told that there was an uneasy relationship between Helen Nicholls, a performance adviser at UK Sport who dealt with cycling, and some UK Sport governance managers, because they felt she put performance before anything else.

It remains a matter of contention how much Nicholls, who regularly met Shane Sutton and other senior figures at British Cycling and reported back to Timson and Warr, was told about a report by Peter King in November 2012, which revealed some of the tensions and problems at the velodrome. British Cycling insiders insist Nicholls was fully briefed by its then chief executive Ian Drake, and that UK Sport could have asked for a full version of the report at any time.

However UK Sport told the Guardian that Drake’s briefing to Nicholls “failed to cover the cultural matters raised in the report which subsequently came to light when we finally received a copy of the King report in June 2016” – and that a written summary received by its chief executive, Liz Nicholl, “also failed to highlight any issues relating to problems regarding the culture.”

The Guardian has learned that the draft version of Annamarie Phelps’ review into the culture of British Cycling is critical of UK Sport in places, saying it “did not dig deep enough into the cultural reality of the World Class Performance Programme” - and “the natural consequence” of that was that neither British Cycling’s board or UK Sport monitored it “in any meaningful way.” However it backs UK Sport’s position that it did not know about the problems within British Cycling between 2012 and 2016.

But multiple sources believe there were ample opportunities for UK Sport to have been aware of any issues within British Cycling even after the 2008 Olympic road race champion Nicole Cooke raised her concerns in 2011. Not only are UK Sport staff routinely in contact with both senior management and the high-performance units in every sport but, every year, all UK Sport-funded athletes are vigorously encouraged to participate in the Athlete Insights Survey, run by a contracted external company, which feeds back anonymous results to UK Sport.

UK Sport has also confirmed that while British Cycling was allowed to self-assess against specific governance criteria in every year since 2008 – it did also receive an onsite audit by AHL Ltd in 2009 and Moore Stephens in 2011 and 2015.

In a statement it added: “It is the norm for these assessments to raise issues for the funded organisation to address – it would be almost unheard of for no recommendations to be made as a result of an onsite audit for example. In British Cycling’s case, issues were raised at each assessment, with correlating recommendations made in order to address the issues.

“UK Sport uses these external assessments as part of the evidence to inform our own internal rating of a sports’ governance, and this is formally assessed each year as part of our investment processes.”