In 1829 Atkinson left India after a disagreement with the newly arrived Governor General Lord Bentinck concerning Atkinson's role at the Government Gazette and he spent the next five years in England.
In 1833 he returned to India resuming his former profession of Surgeon with the HEIC, during which time he had published a translation of Nizami Ganjavi's Laili and Majnun and Makhzan ul Asrar, the Treasury of Secrets by the Oriental Translation Fund in 1836.