The veteran German creator turned the Grand Palais into a forest, with tonnes of dead leaves strewn on mirrored steps and nine tall mossy oaks planted down the middle of its vast nave.
Trees had also been chopped down to make rows of benches for his guests, including Hollywood star Keira Knightley, British pop singer Lily Allen and former French first lady Carla Bruni Sarkozy.
But the France Nature Environment group condemned the show as "heresy", accusing the luxury brand of trying to "give itself a more green image while completely divorced from the reality of protecting nature."
It said that whatever point Chanel was trying to prove with the show "had failed. Nature is not chopping down trees in a forest, putting them up for a few hours for a show and then throwing them into a skip."
Chanel hit back strongly late Tuesday saying none of the oak and poplar trees it sourced from a forest in western France had been a century old.
"In buying the trees Chanel also promised to replant 100 new oak trees in the heart of the same forest," the brand added in a statement.
Chanel raised eyebrows last year for a PVC-themed collection at a time when plastic pollution is hitting the headlines.
Huge life-like forest
Fashion critics had earlier praised the set, with Harper's Bazaar declaring that the "runway may be (Lagerfeld's) best yet". It loved the "life-like forest" he conjured up that "seemed to extend infinitely".
The 84-year-old creator had sent out a dark and classy collection that eschewed the bubblegum girliness of Chanel's haute couture show in January.
The few pinks and electric blues he allowed to seep into the show were confined to handbags and the very Audrey Hepburn leather opera gloves worn with a series of black lace slip dresses.
The final Lagerfeld touch was that the gloves, like his own, were fingerless.
ith his controversial wispy beard that so divided opinion at January's fuller now, the "Kaiser" took one of the briefest bows of his career after the show, allowing photographers little chance to check its progress.
Some critics had then found it shockingly "scruffy" for the world's pre-eminent style guru, who had not changed his look in two decades.
Lagerfeld began the show with a run of full-length black coats matched with sparkling gold tights, one coat feathered at the shoulders and cuffs which gave it more than a hint of French Empire dash.