The letter signed by Rev. Claude Champagne, the president of the Atlantic Episcopal Assembly, says the policy changes are creating hardships, particularly for seasonal workers.
The letter says the bishops want to "express our solidarity," with people who are suffering from losing their benefits during difficult economic times.
The letter acknowledges that some EI reform is needed to curb abuse of the system.
However, the bishops also say the unemployed shouldn't be subjected to "unrealistic regulations to qualify for assistance when it is needed."
Under some of the new rules, those who frequently claim EI need to prove they're actively seeking work.
Workers must also accept a job within 100 kilometres of their home as long as they are qualified and the pay is at least 70 per cent of their previous salary.
The bishops also said in the letter that a call by the Atlantic premiers for a halt to the changes should be considered by Ottawa.
"Some have even asked for a halt to the changes. These warnings need to be taken seriously by all concerned," says the letter.
"May the Holy Spirit of Wisdom prevail in these difficult times."
Federal Human Resources Minister Diane Finley has said that the changes to EI will better connect Canadians with available jobs in their area.
She also has said that her department will take individual circumstances into account.