It also found Labour to be “responsible” for a series of comments made about antisemitism by Ken Livingstone.
The EHRC concluded that the Leaders Office “directly interfered” in a complaint about Jeremy Corbyn’s comments on the antisemitic mural in Tower Hamlets.
The complaint was dismissed as not meeting the threshold for investigation.
An EHRC spokesperson said it was not for the watchdog to decide on how Mr Corbyn would respond to claims about failures under his leadership signalled out in the report.
The equalities watchdog found evidence of political interference in the complaints process, with 23 instances of inappropriate involvement by the leader of the opposition’s office (LOTO) and others in the 70 files looked at.
It said this included LOTO staff influencing decisions on complaints, especially decisions on suspensions or to investigate a claim. Some decisions were made because of likely press interest rather than any formal criteria.
The EHRC said: "The Labour party adopted a practice of political interference in certain complaints and the evidence indicates that it occurred more regularly in antisemitism cases.
“The EHRC has found this to be indirectly discriminatory and unlawful, adding that the practice puts the person making a complaint of antisemitism at a disadvantage as they could face different and detrimental treatment and a risk that their complaint would not be handled fairly.
“A transparent and independent antisemitism complaints process, where all cases of alleged discrimination, harassment or victimisation are investigated promptly, rigorously and without interference is an essential part of the reforms needed to rebuild trust.”
An EHRC spokesperson added their “investigation focused on the Labour Party” and that “blame for antisemitism cannot be put on one person.
But they said “some blame” could be attached to Jeremy Corbyn over failures to deal with the crisis.
The report also contrasted the way sexual harassment complaints had been treated with the failings over antisemtism cases.
The equality body said its analysis points to a culture within the party which, "at best, did not do enough to prevent antisemitism and, at worst, could be seen to accept it.
"This is in direct contrast to the comprehensive guidance and training in place to handle sexual harassment complaints that demonstrates the party’s ability to act decisively when it needs to, indicating that antisemitism could have been tackled more effectively," the EHRC said.
The investigation also stated that the party needed to instil a culture that encouraged members to challenge inappropriate behaviour and to report antisemitism complaints.
The EHRC has warned that, despite some recent improvements, the party must do more if it is going to regain the trust of the Jewish community, the public and many of its members.
It set out "clear, fair and achievable recommendations" to help the party make "positive" changes to its policies, processes and culture.
The new leadership’s commitment to implement the EHRC recommendations was said to be welcome.
The Labour Party has until 10 December to draft an action plan to implement the recommendations, which is legally enforceable by the court if not fulfilled.
Caroline Waters, Interim Chair of the Equality and Human Rights Commission, said: “The Labour Party made a commitment to zero tolerance for antisemitism. Our investigation has highlighted multiple areas where its approach and leadership to tackling antisemitism was insufficient. This is inexcusable and appeared to be a result of a lack of willingness to tackle antisemitism rather than an inability to do so.
“It is encouraging to see the party’s new leadership has committed to implementing our recommendations in full. If the party truly wants to rebuild trust with its members and the Jewish community, it must acknowledge the impact that numerous investigations and years of failure to tackle antisemitism has had on Jewish people, and take swift, sincere action to improve.
“Politicians on all sides have a responsibility to set standards for our public life and to lead the way in challenging racism in all its forms. There have been recent examples of behaviour from politicians of various parties that fall well below the standards we would expect.
"While freedom of expression is essential to proper political debate, politicians must recognise the power of their language to sow division. Our recommendations provide a foundation for leaders to make sure that they adhere to equality law and demonstrate their commitment to diversity and inclusion through their words and actions.”
The probe was launched after complaints from the Campaign Against Antisemitism and a further submission from the Jewish Labour Movement.
The EHRC launched its investigation in May 2019.
