Home Office agencies embroiled in the Windrush scandal have reported rising levels of discrimination in the workplace, an official survey has revealed.

Employees at the Border Force and Immigration Enforcement, which played a key role in the wrongful detention and prosecution of people who rightfully came to the UK from the Caribbean, told an internal survey they face increasing levels of discrimination from colleagues.

The findings raise further questions about a failure by Home Office ministers to address systemic and cultural problems within the department which were highlighted by MPs in March.

The internal survey of civil servants found that more than a fifth of staff at Border Force have experienced discrimination while carrying out their duties – the worst figure for any of the UK’s 89 government agencies and departments.

Four in 10 employees did not agree that Border Force is committed to creating a diverse and inclusive workplace, and the agency also records the worst score of any UK government department for “respecting individual differences”.

Border Force is directly accountable to ministers and is responsible for immigration and customs at 140 rail, air and sea ports in the UK and western Europe.

Staff at Immigration Enforcement (IE), the body whose targets for “illegal immigration” removals were at the heart of the scandal, have reported rising levels of discrimination in the workplace over the past year.

One in every five IE employees (20%) told the civil service people survey they had “personally experienced discrimination at work”.

The Home Office, which resumed direct responsibility for the UK Border Force in 2013, continues to be dogged by accusations of racism and the fallout from the Windrush scandal, which was first highlighted by the Guardian.

In recent months, a group of MPs referred the department to the Equality and Human Rights Commission. The National Audit Office launched a separate investigation into the decision to accuse 34,000 international students of cheating on English language tests, and whistleblowers alleged that a culture of incompetence and bullying had led to failed deportations and the unlawful detention of vulnerable people.

Last month, it emerged the government is still to make compensation payments to Windrush victims 15 months after Theresa May apologised and promised a financial settlement.

The survey was updated with the latest figures on diversity and discrimination in April. It measures staff opinion in around 100 public agencies and around 300,000 employees take part.

It highlights the discontent surrounding discrimination among employees at the Border Force, as new changes to immigration rules after Brexit are expected to exacerbate demand and pressure.

Commenting on the findings, Labour MP for Greenwich and Woolwich, Matthew Pennycook, said: “It is deeply alarming that more than one in five immigration staff have personally witnessed discrimination and harassment at work during the course of the last year. If this is what those who work in these sensitive agencies routinely experience, what chance is there for the often vulnerable people they are employed to serve.

“How can a department found to be the most discriminatory workplace environment in the entire civil service for several years running, convincingly argue it has learnt the lessons of the abomination that is the Windrush scandal, or that it recognises the need to overhaul its toxic culture as well as its systems?

“Ministers must act not only to protect those who work in these sensitive agencies but to fundamentally overhaul our immigration system so those using it can have confidence that it is effective, humane and just.”

A Home Office spokesperson said: “We value all of our staff who work tirelessly to serve the public and keep them safe, and their wellbeing is our priority.”

• This article was amended on 19 August 2019 because an earlier version misnamed the Equality and Human Rights Commission as the Equalities and Human Rights Commission. This has been corrected.