Franco, who has denied claims made by two women, won best actor in a comedy for his role as Tommy Wiseau in The Disaster Artist, but did not collect his accolade.
Hours before the ceremony, further claims were published in the Los Angeles Times by five women who said he had been sexually inappropriate.
Franco did not issue a fresh statement, but his publicist pointed towards the actor’s previous comment that allegations which had been made on social media were “not accurate”.
On the night, the Critics’ Choice Awards honoured women-centric stories like Big Little Lies, The Handmaid’s Tale and The Marvelous Mrs Maisel.
Wonder Woman was named best action movie and star Gal Gadot accepted a special award for challenging gender stereotypes.
She was presented with the second #SeeHer award for furthering the image of women on screen.
Gadot celebrated the success of Patty Jenkins, her director in Wonder Woman, but pointed out there is still a dearth of women directing top movies.
She said: “In the past weeks and months we’ve been witnessing a movement in our industry and society and I want to share this award with all women and men who stand for what’s right.
“My promise and commitment to all of you is that I will never be silenced and we will continue to band together to make strides uniting for equality.”
The Shape Of Water, which stars Londoner Sally Hawkins, was the most celebrated film on the night, winning four awards, including best picture and best director for Guillermo Del Toro.
Del Toro, accepting the best film accolade, brought stars Hawkins and Octavia Spencer to the stage as well as screenwriter Vanessa Taylor.
“For everyone that has been unequal in working with women, let me show you who stands here with us and made this movie possible,” he said.
“Let me tell you one thing: you don’t know what you’re missing.”
Here is the full list of winners:
Best picture – The Shape Of Water
Best actor – Gary Oldman, Darkest Hour
Best actress – Frances McDormand, Three Billboards Outside Ebbing, Missouri
Best supporting actor – Sam Rockwell, Three Billboards Outside Ebbing, Missouri
Best supporting actress – Allison Janney, I, Tonya
Best acting ensemble – Three Billboards Outside Ebbing, Missouri
Best director – Guillermo Del Toro, The Shape of Water
Best original screenplay – Jordan Peele, Get Out
Best animated feature – Coco
Best action movie – Wonder Woman
Best comedy – The Big Sick
Best actor in a comedy – James Franco, The Disaster Artist
Best actress in a comedy – Margot Robbie, I, Tonya
Best sci-fi or horror movie – Get Out
Best comedy series – The Marvellous Mrs Maisel
Best actor in a comedy series – Ted Danson, The Good Place
Best actress in a comedy series – Rachel Brosnahan, The Marvellous Mrs Maisel
Best supporting actor in a comedy series – Walton Goggins, Vice Principals
Best supporting actress in a comedy series – Mayim Bialik, The Big Bang Theory
Best drama series – The Handmaid’s Tale
Best actor in a drama series – Sterling K Brown, This Is Us
Best actress in a drama series – Elisabeth Moss, The Handmaid’s Tale
Best supporting actor in a drama series – David Harbour, Stranger Things
Best supporting actress in a drama series, Ann Dowd, The Handmaid’s Tale
Best limited series – Big Little Lies
Best movie made for TV – The Wizard of Lies
Best actor in a movie made for TV or limited series – Ewan McGregor, Fargo
Best actress in a movie made for TV or limited series – Nicole Kidman, Big Little Lies
Best supporting actor in a movie made for TV or limited series – Alexander Skarsgard, Big Little Lies
Best supporting actress in a movie made for TV or limited series – Laura Dern, Big Little Lies
Best talk show – Jimmy Kimmel Live!
Best animated series – Rick And Morty