He advised Lord Auckland to support Dost Mohammed on the throne of Kabul, but the viceroy preferred to follow the opinion of Sir William Hay Macnaghten and reinstated Shah Shuja, thus leading to the disasters of the First Afghan War.
It came to light in 1860 that some of Burnes' dispatches from Kabul in 1839 had been altered to convey opinions that had not been his, but Lord Palmerston refused after so long to grant the inquiry demanded in the House of Commons.