In a statement, police said there was evidence to prosecute two other former staff members, including Leeks, but the pair weren't fit to stand trial.
A former patient of the unit, Paul Zentveld, said the decision to lay charges meant it finally felt as if survivors were listened to.
"It's better than nothing, that's all I can say. [It's] better than calling us liars, saying we made it up and were imagining things that never happened at Lake Alice."
The decision comes after apologies to survivors from the Medical Council, Crown Law and police, over aspects of their previous investigation in 2002-2010.
No charges were laid then or after another investigation in the late 1970s.
Zentveld said police never interviewed him for their previous investigation, but had since told him there was enough evidence to lay charges from his statement alone.
He was given drugs and electric shock treatment as punishment for minor misdeeds during his five admissions to the Lake Alice unit.
His pursuit of justice has taken him to the United Nations Committee Against Torture, which last year upheld his complaint.
It urged the government to investigate, leading to the Royal Commission of Inquiry into Abuse in State Care this year hearing evidence from former patients at the unit, which operated at the Rangitīkei institution.
Many said they were subject to abuse at the hands of Leeks, or at his instigation.
Independent watchdog group, the Citizen's Commission on Human Rights, helped Zentveld with his UN claim and has investigated Lake Alice since 1976.
Commission director Mike Ferriss said charging the former staff member was recognition of what former patients had long said.
It was important police had said they had enough evidence to charge Leeks, and survivors would like to know what charges he would have faced.
"To them, that would have added some weight to the closure of this sad and sorry event," he said.
"Of course it matters to the survivors that Leeks isn't facing charges, but I think people understand that the police are bound by certain rules that prevent that from happening, given Dr Leeks' dementia."
The Auckland Committee on Racism and Discrimination has also long worked to achieve justice for former patients. Founding member Dr Oliver Sutherland says Leeks has been let off the hook.
"For 50 years we've waited and we've just ended up with a single person appearing before the court. It's some vindication, but it's not a satisfactory outcome I don't think."
Police said their latest investigation, which began in February 2020, included interviews with 63 former patients and more than 46,000 pages of evidence.
"Police acknowledges the enormous impact these events have had on the lives of those former patients who were children and young people at Lake Alice in the 1970s, and the frustration of those who have been waiting for us to complete this investigation," said officer in charge, Detective Superintendent Tom Fitzgerald.
"This operation involved unprecedented mass allegations, with complex legal arguments and expert medical evidence, so it was vital that we undertook a methodical and meticulous approach with thorough consideration of culpability."
A statement from the Royal Commission said it understood Lake Alice survivors would be disappointed with the decision not to charge Leeks.
But, commission chairwoman Coral Shaw said, it didn't mean the inquiry couldn't make adverse findings against him.
"Importantly, we will also make findings about how the allegations were dealt with by authorities, including NZ Police."
The commission report is due in June 2023.
