Victoria's top policeman will meet with Facebook over concerns the site's users incite hatred and undermine the criminal justice system.

Chief Commissioner Ken Lay will meet with the head of Facebook Asia on Wednesday following his concerns that hate pages could have threatened the high-profile prosecution of Adrian Ernest Bayley, the Melbourne man accused of raping and murdering Melbourne woman Jill Meagher last year.

"It's my understanding that some Facebook management were a little concerned about my comments about the ethics of Facebook so they were keen to meet with me and put their point of view," Mr Lay told Fairfax Radio on Wednesday.

Mr Lay, who described some of the comments posted regarding the Jill Meagher case as "absolute garbage", said he was pleased the social media site would meet with him.

"I need to understand how we can hold Facebook to account when I believe they act inappropriately," he said.

Mr Lay said it was difficult to enforce laws when much of Facebook's content was managed offshore.

He said the case of a 16-year-old girl who had a photo taken of her at the beach which ended up on a sexually suggestive site on Facebook, was another example of concern.

"This is but another example of just how difficult it is to control some of the stuff on Facebook, when a 16-year-old girl finds herself unwillingly on a site like this and my understanding is the people that control the site have basically said stiff, we're not changing it," he said.

"It's not tolerable.

"It's just fortuitous that later on today I'm meeting the head of Facebook Asia who is going to explain to me how the Jill Meagher issue occurred and how we can work our way through this.

"I will again raise this issue with him to try and better understand how people's privacy can be protected by Facebook."

Bayley, 41, is due to face the Melbourne Magistrates Court later in January.

Facebook has previously said it would remove content when it violated local law.