The 15-year-old disappeared in 1994 after a school disco in County Donegal.
Norman Baxter, a retired PSNI detective superintendent, took over the inquiry for a few weeks in  2002.
He offered a frank and damning assessment of how the Arkinson family had not been helped.
When he took over the inquiry, the schoolgirl had been missing for eight years and Mr Baxter told the inquest the status of the investigation was "vague - neither closed nor active".
He said he was determined to progress it, with the help of other committed officers already working on the case.
Speaking of Arlene, Mr Baxter said: "I would say she was a forgotten victim.  That's quite a terrible thing."
He added: "I think it's terrible that a 15 year old vanishes and, after a period of statutory obligation, you park it and move on."
He told the inquest how he was able to charge the prime suspect Robert Howard with her murder within two months of taking over, despite his team having uncovered no major new evidence.
Mr Baxter explained he had worked on other similar cases and observed other inquiries where murder charges had been pressed, even without a body.
"My predecessors took the view that if there's no body, there's no murder charge," the retired officer said.
Changes in how police viewed such cases meant that he was able to charge Howard with Arlene's murder on 24 May 2002.
The court heard that Howard lost control after he was charged and began to suggest that he might help officers locate Arlene's body.
Within hours, Mr Baxter said, Howard had indicated to him that he might cooperate with the police and had asked where he might serve his sentence.
The former officer described Howard during that meeting as "extremely agitated", "totally dishevelled" and "very very unsettled.", telling the court that "he certainly had lost control".
After being told he would likely be kept in Belmarsh prison on remand, the court heard that Howard asked if he might be allowed to serve his sentence at Maghaberry prison in Northern Ireland, which he thought offered better conditions.
By this time he had also been charged with the murder of 14-year-old English schoolgirl Hannah Williams in 2001.
Her body had been found in Kent in 2002, a few weeks before Howard was brought to Northern Ireland to be interviewed by the Police Service of Northern Ireland.
Mr Baxter said he had viewed the site where Hannah's body had been buried, and had cooperated closely with Kent Constabulary.
At one stage, he added, Kent Constabulary told him him they had considered dropping charges connected to Hannah Williams if Howard had cooperated with the PSNI in finding Arlene's body.
Mr Baxter told the court he did not believe this idea had been communicated to Howard.
He said Kent Constabulary had carried out "a pre-emptive arrest and charging" of Howard, hoping to hold him until the PSNI could charge him with the murder of Arlene Arkinson.
Later, new stronger evidence emerged in the Hannah Williams case and Howard was ultimately convicted of her murder.
Howard faced a trial in Northern Ireland for Arlene's murder in 2005, but was acquitted by a jury which, for legal reasons, had been unaware of his previous convictions.
Later Mr Baxter told the court more about the child killer.
He said he was amazed that some officers initially investigating Arlene's disappearance had not been told that Howard was already on bail for serious sexual offences.
"Everywhere he went, he was a menace" said Mr Baxter.
"Violent sexual depraved behaviour and the state was ineffective to deal with it."
Robert Howard died in prison in England last year.
A senior detective who briefly led the inquiry into the disappearance of Arlene Arkinson has told an inquest that Robert Howard could have been charged years earlier.