A number of fishermen went back out on the water after they had tied up their boats, even though processors have said they can't afford to pay them more.
"Obviously, we are concerned by what we're seeing in the marketplace," Harper said after an announcement in Summerside, P.E.I.
"We obviously encourage the fishermen and processors to work to find a solution to some of the market difficulties in this particular area."
A group of Nova Scotia fishermen voted 196-52 to untie their boats at a meeting Monday in Antigonish.
Dan MacDougall, president of the Gulf Nova Scotia Bonafide Fisherman's Association, said he believes the show of unity by Maritime fishermen will send a message to buyers and processors.
"We did something here that hasn't been seen in these parts that I know of — fishermen standing beside and behind each other on a common goal," he said.
Still, MacDougall said there is more work to be done to improve prices at the shore.
Ronnie Heighton, president of the Northumberland Fisherman's Association, said the stress and frustration of the past several days will be worthwhile if the pricing system is improved.
In Prince Edward Island, fishermen between Souris and Tignish also voted to return to the water Tuesday to salvage what's left of their two-month season, but some fishermen in southern areas were still holding out.
Fisheries ministers in the Maritimes have said they plan to sit down and examine the pricing structure for lobsters.
In Nova Scotia, Fisheries Minister Sterling Belliveau said Monday night he hopes to meet with his counterparts from P.E.I. and New Brunswick later this week. He also suggested creating a panel to address the issue after meeting Monday with fishermen in Truro.
The meeting came after fishermen tied up their lobster boats more than a week ago to draw attention to prices that have dipped to about $4 a pound in Nova Scotia and as low as $3.25 in P.E.I.
Some fishermen say they are looking for prices similar to what they were getting last year, at around $4.50 to $5 a pound.
Michael McGeoghegan of the P.E.I. Fisherman's Association said the protest has highlighted the problematic pricing structure for consumers who buy lobster in grocery stores.
"We've always known that amongst fishermen but the general public hasn't known that," he said.
(ECFM, The Canadian Press)