Harper was asked about outmigration and what, if any, relationship it may have to EI changes while he was in Prince Edward Island, a province where those changes have been met with protest.
"To the extent that there's outmigration, it has nothing to do with the employment insurance system," Harper said after a funding announcement in Charlottetown.
"It is just the reality, and it's not unique to Prince Edward Island, that there are greater economic opportunities, particularly for young people, more economic opportunities in some parts of the country than others."
Afterwards, Premier Robert Ghiz repeated his demand that the federal government reverse the changes, saying he is concerned they will hurt his province's seasonal industries.
"As Atlantic premiers, we all believe that the changes ... have not been good for Atlantic Canada," Ghiz said, adding that he was not given an opportunity to meet with the prime minister.
"We continue to make evidence-based research available to the federal government to be able to demonstrate that we think it has more of a negative impact in terms of provinces where seasonal industries play a larger role."
Ghiz said the Atlantic premiers are studying a draft of a report they commissioned to determine the impact of the changes. He said the report concludes that it has been difficult to measure the impact because the changes were introduced only last year.
"But it calls for a reversal of some of the changes that were implemented," Ghiz said, citing contentious provisions regarding eligibility, which he says have created a two-tier system on the Island.
As for outmigration, Ghiz did not challenge Harper's assertion, saying the empirical evidence is still being gathered.
"You need to see research to be able to demonstrate that is true," he said. "I haven't seen that research yet.
"I agree with the prime minister: if there's work available, then people should be working. I agree that the EI system is not perfect. But I think we should be going about (changing) it in a manner that is respectful of different jurisdictions across the country."
Harper said the federal government has been monitoring the changes and a "minuscule" number of people have been disqualified from receiving EI since the changes were implemented in January 2013.
"These are obviously cases where people are simply not eligible," he said.
Under the changes, people must 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 changes have prompted numerous protests across Atlantic Canada.
The federal government has said the changes will better connect people with available job opportunities and they were required as a result of unprecedented labour and skills shortages.
The changes to the program are expected to save the public treasury $33 million this year.
Note to readers: This is a corrected story. A previous version wrongly said a long-standing requirement was a change. That requirement is that those who frequently claim EI need to prove they're actively seeking work.