The UN’s environment chief, Erik Solheim, has resigned following severe criticism of his global travels and internal rule-breaking which led some nations to withhold their funding.

The Guardian understands Solheim was asked to resign by the UN secretary general, António Guterres. Sources at the UN Environment Programme (Unep) said that countries unhappy with Solheim’s conduct were holding back tens of millions of dollars, threatening a financial crisis at the body.

A draft internal UN audit leaked to the Guardian in September found Solheim had spent almost $500,000 (£390,000) on air travel and hotels in just 22 months, and was away 80% of the time. The audit said this was a “reputation risk” for an organisation dedicated to fighting climate change.

A UN staff union leader called some of the revelations “mind-blowing” and a prominent climate scientist accused Solheim of “obscene CO2 hypocrisy”.

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The audit said Solheim had “no regard for abiding by the set regulations and rules” and had failed to account properly for some of his travel. He also unofficially allowed chosen staff to work from Europe rather than at Unep headquarters in Nairobi, Kenya. Solheim told the Guardian he had already paid back money for instances of oversight and made changes where other rules had been broken.

On Tuesday, the UN secretary general’s official spokesman said Guterres had accepted Solheim’s resignation. “The secretary general is grateful for Mr Solheim’s service and recognises he has been a leading voice in drawing the world’s attention to critical environmental challenges.”

The final version of the internal audit report has yet to be made public, but the spokesman said: “The secretary general is pleased to see that Unep is committed to implementing the recommendations that are found [in the report].” Unep’s deputy executive director, Joyce Msuya, has been appointed acting head while a replacement is sought.

The Guardian had also revealed that Solheim had to recuse himself in September from professional dealings with his own wife and a Norwegian company that employed her shortly after it signed a deal with Unep in April.

The Netherlands, Denmark and Sweden are among the countries that publicly said they were halting funding for Unep until the issues around Solheim were resolved. The total sum at stake is in the region of $50m, according to sources.

Some staff at Unep have been deeply unhappy with Solheim’s leadership for a long time. At a meeting between Solheim and staff in Nairobi in September, of which the Guardian has seen a recording, Tim Christophersen, the head of the freshwater, land and climate branch at Unep, said: “Some of the work in my branch basically has hit a bit of a wall, because the donors we speak with are freezing their contributions to the environment fund.

“None of us individually is more important than the UN,” Christophersen told Solheim. “What should not happen in this organisation is that people are allowed to put their personal agenda ahead of the organisation, whether this is where you prefer to live, how you prefer to travel.”

Numerous Unep staff have contacted the Guardian criticising Solheim’s perceived closeness to China and the project he initiated related to the environmental sustainability of China’s huge infrastructure Belt and Road Initiative. The US in particular was concerned and its representatives raised a long list of questions as far back as April, including about how the project was funded and how intellectual property rights would be protected.

Another concern to staff was the $500,000 sponsorship Solheim agreed to give the Volvo Ocean Race, despite it not being mentioned on the VOR sponsors’ web page or announced by Unep.

Solheim emailed staff on Tuesday and said: “I wanted UN Environment to be a lead agency for reform, even if it raised some questions. Doing things differently is never easy and I will depart knowing I never spared a moment in my effort to implement this vision and leave UN Environment more capable and more impactful.”

One senior employee welcomed Solheim’s resignation: “It will let us get on with the job we have to do, which is a big one. This was getting in the way.”

The crisis had prompted Solheim to lead a three-day retreat last week with senior directors. He emailed staff on Monday: “We agreed on and committed to a set of principles [to] guide the way we work and interact with each other.” But on Tuesday, he was gone.