A senior civil servant at HM Revenue & Customs has been sacked after facing a catalogue of sexual misconduct claims by five junior female employees, the Guardian has learned.

Mark Nellthorp was dismissed from his position as a deputy director at the government tax body in September after some of the grievances were upheld.

Three of the women who made complaints about Nellthorp are understood to have claimed they were sexually assaulted as well as harassed. The five women are based in offices across the country to which Nellthorp travelled in his London-based post.

Nellthorp, who is in his late 50s, was also interim chair of Portsmouth Hospitals NHS trust from June 2017 to the end of October that year, during which period some of the alleged sexual misconduct is said to have occurred at HMRC.

As a public face of the trust, which has an annual turnover in excess of £500m and employs more than 7,000 staff, he gave out awards to staff at annual ceremonies. He served on the trust’s board from 2007 until late 2017.

Nellthorp is fighting one employment tribunal claim of sexual harassment brought by one woman against both him and HMRC.

Two female assistant directors at HMRC who worked closely with Nellthorp were suspended on full pay last February after being accused of helping facilitate his behaviour. They are still being investigated.

A more junior HMRC employee has been sacked after being accused of enabling Nellthorp’s behaviour.

Concerns have been raised that HMRC, which has more than 60,000 staff nationwide, is failing to deal with a culture of bullying and harassment. The latest staff survey results show that 14% of HMRC’s workforce say they have suffered bullying and harassment – higher than the civil service average of 11%.

In November, HMRC launched a “respect at work” review chaired by a former John Lewis HR director, Laura Whyte, which is looking into procedures for dealing with bullying and harassment claims. It is understood the review was prompted by the Nellthorp case.

After being contacted by the Guardian, HMRC on Friday published the review’s report, which recommended an “urgent redesign of the grievance process” including more use of “mediation and early resolution”, among other changes.

It said the review did not find “any individual within HMRC who had confidence in the grievance process”. Staff felt they tolerated a lot of “low-level poor behaviours” not accepted in other workplaces, including swearing, breaching confidentiality and mocking colleagues.

Nellthorp worked at HMRC for more than a decade, rising to the rank of deputy director overseeing investigations into tax avoidance. In 2007, he gave evidence at a committee hearing at parliament on behalf of HMRC.

The Guardian understands that concerns about Nellthorp’s behaviour were known to HMRC for some time. About three years ago a formal complaint about bullying was made against him. The complaint, understood not to relate to any sexual misconduct, was dealt with internally and was not upheld.

HMRC first received a complaint from one of the alleged victims about sexual harassment on 19 December 2017. Separately, the Guardian understands, an anonymous complaint to HMRC was made about his conduct in October 2017. It was not until February 2018 that he was suspended from his position.

HMRC’s investigation into Nellthorp’s behaviour heard a series of allegations about misconduct both in and outside the workplace from complainants and colleagues.

Nellthorp, who is understood to be appealing against his sacking, hung up when the Guardian rang him for comment. He did not respond to further requests.

Esther Wallington, HMRC’s chief people officer, said: “Sexual misconduct and bullying of any kind have absolutely no place in a modern and diverse organisation such as HMRC. When serious accusations were made recently which led to gross misconduct being found, we didn’t hesitate to take firm action resulting in dismissal.

“While we have no evidence of widespread serious misconduct, we will not rest until we are satisfied that all our staff work in an environment free from bullying, harassment and sexual misconduct. Last year, we commissioned an independent, thorough review into how we handle and respond to such accusations across HMRC and are speaking directly to our people about its findings to ensure that all our staff work in a safe and positive environment.”

Pictures on the Portsmouth NHS trust’s Facebook page show Nellthorp giving out framed certificates to staff at its annual “best people awards” in 2015, 2016 and 2017.

He last attended a meeting of the trust’s board in November 2017 as a non-executive director, and minutes recorded that “he will be leaving the trust at the end of November”. No reason was given for his departure.

The trust said he left the board at the end of his tenure and neither he nor HMRC had made it aware of the allegations against him.

A spokeswoman said: “The trust was made aware of allegations against Mark Nellthorp several months after he had left his roles. We immediately contacted HM Revenue & Customs, who confirmed that they were conducting an ongoing investigation into allegations against Mark Nellthorp while he was employed at HMRC.

“We took swift action to assure ourselves that the trust had received no reports of similar allegations against Mr Nellthorp during his time as a NED [non-executive director] or interim chairman. A full and comprehensive recruitment process was undertaken prior to Mr Nellthorp being appointed to his role at the trust, which included a Disclosure and Barring Service check.”

No similar complaints were received by the trust during his tenure and he had limited contact with patients, the spokeswoman said.

A spokesman for the Public and Commercial Services Union, which represents HMRC civil servants, said: “The PCS opposes all forms of discrimination and harassment and condemns it in the strongest possible terms. We will support members affected by this case, and due to the sensitive nature of the issues raised in this article we will not be commenting further.”

A separate Guardian investigation in November revealed that HMRC had received 362 complaints from staff about alleged sexually harassment and bullying since 2016, and that only a fraction of staff had faced disciplinary investigations as a result.

At least 68 female staff made sexual harassment complaints and 294 HMRC staff made complaints about being bullied by colleagues.

After being approached by the Guardian, the HMRC on Friday released its “respect at work” review, which recommended an urgent redesign of the grievance process, including among other changes a greater use of “mediation and early resolution”. It followed the review not finding “any individual within HMRC who had confidence in the grievance process”.

The report also noted the need for improvement after establishing staff tolerated “low-level poor behaviours” not accepted in other workplaces, including swearing, the breaching of confidentiality and the mocking of colleagues.