Police have admitted that the managers of an undercover officer who deceived a woman into a long-term sexual relationship knew about it and allowed it to continue, legal papers have revealed.

It is the first such admission by police chiefs, who had claimed that their undercover officers were not allowed to have sexual relationships with campaigners they were spying on under any circumstances.

The admission was made by police in a legal case launched by Kate Wilson, an environmental and social justice activist who was deceived into a two-year intimate relationship by the undercover officer Mark Kennedy.

She did not discover his true identity until he was exposed in 2010 by campaigners who found out that he had spent seven years infiltrating environmental groups.

Wilson is taking legal action against the Metropolitan police and the National Police Chiefs’ Council in the investigatory powers tribunal (IPT), a court that examines allegations that the state has abused its surveillance powers and infringed people’s human rights. She is alleging that police violated her human rights in five ways.

It is the first case to be heard by the IPT from a woman who had a sexual relationship with a police spy who concealed his true identity from her.

Wilson is one of at least 12 women who have successfully sued police in high court cases but says she wants to continue her fight for the truth by taking the case to the IPT.

After a lengthy legal battle in the high court, the Met was forced to pay compensation to the women, although it successfully avoided handing over any internal documents about the relationships.

In an apology to most of the women, the Met admitted the relationships had been “abusive, deceitful, manipulative and wrong” and claimed the “forming of a sexual relationship by an undercover officer would never be authorised in advance”.

Writing in the Guardian on Friday, Wilson said: “Now I really want answers. I want to know how high up the police hierarchy knowledge of the abuses went.”

In papers lodged with the IPT, the police admitted that Kennedy’s cover officers and line manager “were aware that he was conducting a close personal relationship” with Wilson. They added that Kennedy’s “sexual relationship with [Wilson] was carried out with the acquiescence of his cover officers and line manager”.

The police admitted Kennedy’s deception violated Wilson’s human right not to be subjected to inhumane and degrading treatment and that the severity of the violation was exacerbated because supervisors allowed him to continue the relationship.

In a statement, Wilson said: “It has taken me eight painful years to discover that managing officers really did conspire to deceive and abuse me, something the police had consistently denied.

“The wide questions for society here are massive, this is about institutional sexism, senior police officers sanctioning sexual abuse, and the systematic violation of political beliefs, and we still don’t have the whole truth.”

Wilson started her relationship with Kennedy in 2003, early in his deployment, when she was involved in organising protests against a summit of G8 leaders in Scotland.

She has described how he “was charming and disarming. He shared my interests and my passion for the political things that we were doing. He told me lots of his most intimate stories and secrets.

“He became very close to my parents. He spent many nights in their home. He attended my grandmother’s ninetieth birthday party. He met my entire extended family.”

Investigations by the Guardian and activists have revealed that undercover officers sent to spy on campaigners regularly formed intimate relationships with women without disclosing their real identity.

Kennedy, who used the alias of “Mark Stone” during his covert deployment, is one of more than 140 undercover officers known to have been deployed by police to infiltrate political groups since 1968. He had had a number of sexual relationships using his fake identity.

In her claim, Wilson said she believed that at least six undercover officers spied on her over a decade, playing “different false parts in [her] life, ranging from lover, to close friend and sometime housemate, and co-activist”.

The Met said it “has made clear its position on long-term, sexual relationships known to have been entered into by some undercover officers in the past. Those relationships were wrong and should not have happened.”

At the next hearing of the IPT case on 3 October, Wilson’s lawyers will press the police to disclose official documents about the deception, including the involvement of senior officers – a move being resisted by the police.

In a separate development, a public inquiry examining the conduct of the undercover officers said on Thursday that one of the officers may have used the identity of a five-year-old boy who died in a plane crash.

Kevin Crossland died with his sister and mother in the crash in Yugoslavia in 1966. The inquiry, led by a retired judge, Sir John Mitting, is examining whether an undercover officer who infiltrated animal rights groups between 1997 and 2002 used Kevin’s identity.

Undercover officers routinely stole the identities of dead children to develop their fake personas. However, the inquiry said the theft of Kevin’s name did not appear to have been sanctioned by the officer’s superiors.