Her colleague Ricky Tomlinson - who plays her father, the arch slob Jim - was named best actor and the programme was named top sitcom.
Other major winners were Paul Merton, who was named best entertainment personality, and Sacha Baron-Cohen, Channel 4's Ali G, who was best male newcomer.
Jessica Stevenson - another star from The Royle Family, who also appeared in Channel 4's Spaced - took the female newcomer award.
Aherne came up with the show, which revolves around a working-class Manchester family as they chat in front of their television, after finding success with her spoof chat show host Mrs Merton and on BBC2's The Fast Show.
The Royles missed out on only one title for which they were nominated. Craig Cash, who plays Denise's husband Dave, lost out to Baron Cohen for the newcomer title.
Victoria Wood's BBC1 show dinnerladies was named best new TV comedy at the ceremony, held at London Weekend Television.
ITV's bittersweet Cold Feet took the title for best comedy drama.
There were lifetime achievement award for the Two Ronnies - Ronnie Corbett and Ronnie Barker - and Barry Humphries, best known for his superstar creation Dame Edna Everage.
The awards in full:
Best Television Comedy Actor: Ricky Tomlinson (The Royle Family).
Best Television Comedy Actress: Caroline Aherne (The Royle Family, Mrs Merton & Malcolm).
Best Comedy Entertainment Personality: Paul Merton (Room 101, Have I Got News For You).
Best Live Stand-up: Bill Bailey (The Comedy Store 99/Edinburgh 99).
Best Male Comedy Newcomer: Sacha Baron Cohen (Ali G from The 11 O'Clock Show).
Best Female Comedy Newcomer: Jessica Stevenson (Spaced, The Royle Family).
Best New TV Comedy: dinnerladies (BBC1).
Best Broken Comedy Show: Big Train (BBC2).
Best Comedy Gameshow: Have I Got News For You (BBC2).
Best Comedy Talkshow: So Graham Norton (Channel 4).
Best TV Sitcom: The Royle Family (BBC2).
Best TV Comedy Drama: Cold Feet (ITV).
Best Comedy Film: Notting Hill.
Best International Comedy Show: The Larry Sanders Show (BBC2).
Best Comedy Entertainment Programme: Comic Relief 1999 (BBC1).
Best Radio Comedy: The Sunday Format (BBC Radio 4).
Writer Of The Year Award: Richard Curtis.
Lifetime Achievement Awards: Barry Humphries, The Two Ronnies.Reuse content