Harper, who was in Summerside, P.E.I., for a funding announcement, said it's false to claim that the new rules the Conservative government have introduced are harming people who can only find work for part of the year.
"Let me be very clear in terms of any misinformation, there is nothing, absolutely nothing in our changes that targets seasonal industries or seasonal workers or requires anybody to leave their region to get a job," he said.
"We are simply making sure that when jobs are available that Islanders can fill them and when there is no work for Islanders in their region and they've paid into the fund, they will be eligible to receive."
The changes have stoked protests in the region. Just two weeks ago, Atlantic Canada's premiers asked Ottawa to suspend them, accusing the federal government of implementing the new measures without consultation.
The premiers, who span the political spectrum, said there should be further study of the new rules that took effect in January because they're harming seasonal-based industries that serve as the bedrock for the region's economy.
A spokesman for P.E.I.'s Department of Innovation said the number of people employed goes up almost 19 per cent between January and June, compared to the national average of 4.8 per cent for the same time period. The increase is mostly due to seasonal work in the forestry, construction, fisheries and tourism sectors, Sandy Stewart said.
The premiers have agreed to study the effects of the changes and present interim findings to the annual meeting of Canada's premiers in July. They plan to have the final results of their study complete by mid-fall.
The Roman Catholic bishops in Atlantic Canada have also voiced their opposition, saying some of the region's most vulnerable are suffering from reduced income.
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 federal government has estimated that changes to EI will save the public treasury $12.5 million this year and $33 million next year.
Harper said he realizes finding work can be challenging in Atlantic Canada, but added that his government is committed to stimulating job growth.
"We know that unemployment is still high in this region and that's why we put specific emphasis on making sure we get investments in places like Atlantic Canada," he said.
Harper's comments came after he announced about $7.7 million for three Charlottetown companies in an effort to help them bring their products to the marketplace and create jobs.
Pharmaceutical company BioVectra Inc. will get close to $3 million to develop two generic drugs and Delivra Inc. will be given $2.9 million to support its research on topical creams to relieve pain.
About $1.9 million will go to Island Abbey Foods Ltd. so it can expand a line of honey-based products for therapeutic purposes.
The announcement was part of a wider renewal of the Atlantic Innovation Fund, with a total of $39.9 million allotted for 17 projects across Atlantic Canada.
The remaining 14 projects will be announced in the coming weeks, the federal government said, with $11.4 million set aside for New Brunswick, $11.3 million for Nova Scotia and another $9.4 million going to Newfoundland and Labrador.
Note to readers: This is a corrected story. A previous version reported that P.E.I.'s Department of Innovation said about 19 per cent of workers in June are seasonal employees.
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