Scott Phillip White has been charged with the murder of Scott Johnson, who was found at the base of a cliff near Manly's North Head on December 10, 1988.

The 49-year-old did not appear when his matter was mentioned briefly at Parramatta Local Court on Wednesday.

He did not apply for bail and he will next face court in July.

His arrest represents a major breakthrough in Mr Johnson's family's 32-year fight for justice and follows three inquests into the death.

He was arrested on Tuesday at a Lane Cove property in Sydney's northern suburbs and was taken to Chatswood Police Station where he was charged.

Police said White had been spoken to during their two-year investigation and when asked about his reaction upon his arrest, Detective Chief Inspector Peter Yeomans said: "It wasn't one of surprise."

A $1 million reward for information was offered by police in 2018 before Mr Johnson's US-based brother Steve pledged to match that figure in March.

NSW Police Commissioner Mick Fuller said the $2 million reward was influential in the breakthrough.

"There's certainly one witness, on conviction, that would be eligible for part of the reward absolutely," Mr Fuller told reporters.

The 27-year-old's death was ruled a suicide at the first inquest before a second inquest in June 2012 returned an open finding.

However, the third inquest in 2017 found Mr Johnson fell from the clifftop as the result of violence by an unidentified attacker who perceived him to be gay.

"I do think the plight of young gay men in Sydney, and probably around the world, was a very difficult one and not only were they let down by police, they were let down by the community and probably the media," Mr Fuller said.

"I apologised to Steve Johnson and I've apologised to a number of communities about mistakes that we have made in the past."

Mr Fuller said it had been an "enormous journey" and the findings of coroner Michael Barnes during the third inquest were crucial to re-opening the case two years ago.

Australian Associated Press