Many of the live action scenes were filmed in Australia. Luckily, the rabbits were not real, as they are an introduced pest in Australia (in the 1800s, the country was overrun with rabbits) and live rabbits cannot be brought into the country, with very few exceptions.
In the 1930s, Walt Disney considered doing an adaptation of Peter Rabbit after Snow White and the Seven Dwarfs (1937), but author Beatrix Potter turned down the offer.
According to director Will Gluck, the live-action scenes took about 60 days to shoot, the length of a normal movie shoot. The animation started during filming and took almost 12 months. They finished in early February 2018, only six days before the film came out.
Live action cast members Domhnall Gleeson, Rose Byrne, and Sam Neill also voice some of the animal characters in the film: Mr. Jeremy Fisher, Jemima Puddle Duck, and Tommy Brock, respectively.