Mr Barr said prosecutors should only look into “substantial allegations” of irregularities.
He acknowledged that individual states had the primary responsibility for the conduct of elections but said the justice department had “an obligation to ensure that federal elections are conducted in such a way that the American people can have full confidence in their electoral process and their government”.
The department would normally only go beyond preliminary investigations after an election had been concluded and the results certified, but Mr Barr said this could result in situations where “misconduct cannot realistically be rectified”.
Mr Pilger said he had quit in response to Mr Barr’s memo.
“Having familiarised myself with the new policy and its ramifications… I must regretfully resign from my role,” he wrote in an email to colleagues.
Mr Pilger became head of the department’s Election Crimes Branch in 2010. This branch, and Mr Pilger himself, were previously in the public eye at the time of a row about extra scrutiny of political groups seeking tax exemption.