The Edinburgh-based writer whose Case Histories detective novel was adapted into a TV series starring Jason Isaacs, won the prize for Life After Life, set in wartime Britain.
The prize comes 20 years after Atkinson's first novel, Behind The Scenes At The Museum, was crowned overall winner of the same prize, winning book of the year.
The Costa awards are divided into five categories: first novel, novel, biography, poetry and children's book, with winners of all sections eligible for book of the year, to be announced later this month.
If Atkinson goes on to win book of the year again she will become the first female author to do so twice, with Seamus Heaney and Ted Hughes the only two authors to have won the overall prize twice.
The Shock Of The Fall, the debut penned by a former mental health nurse Nathan Filer, 32 - who now teaches creative writing, has won the first novel award.
The book - the story of a teenagers's descent into madness as he confronts his role in the boyhood death of his older brother - was snapped up by HarperCollins for a "substantial" six-figure sum.
Writer and TV presenter Clive James was on the shortlist to win the poetry prize for his translation of Italian poet Dante, but has been beaten to the award by poet Michael Symmons Roberts - who has won the poetry award for the second time, this time with his sixth collection Drysalter.
The children's book award has been won by political cartoonist, author and illustrator Chris Riddell for Goth Girl And The Ghost Of A Mouse.
Lucy Hughes-Hallett was named winner of the biography award for The Pike, an account of the life of poet Gabriele D'Annunzio.
Bookmakers William Hill made Hughes-Hallett favourite to win book of the year at 2-1, followed by Atkinson at 5-2.
Organisers said that if Hughes-Hallett or Atkinson go on to win the overall book of the year, then women will have won all recent major literary awards.
The winners of each category receive £5,000 with an overall winner getting a further £30,000 at this month's ceremony in central London.
The Costa, formerly the Whitbread, is open to authors resident in the UK and Ireland.