In a statement, the premier said the prime minister "confirmed an endorsement" of the Muskrat Falls project.
"We will continue to work toward a finalization of the details of the federal loan guarantee as expeditiously as possible."
Dunderdale said the two also discussed a number of other issues including the economy, changes to Employment Insurance, and search and rescue.
A short statement from the Prime Minister's Office said Harper "reiterated the federal government's support for the Lower Churchill project."
Dunderdale requested a meeting with Harper in the spring after a public outcry over search and rescue cuts in the province and the death of Burton Winters. The 14-year-old Labrador boy was found dead in February, three days after getting lost in a blizzard.
'At odds' with Peter MacKay
In May, Dunderdale said she was growing increasingly frustrated with Defence Minister Peter MacKay, whose responsibilities include search and rescue.
"I'm certainly at odds with Minister MacKay,” Dunderdale told CBC Radio’s The House in an interview at the time.
"Certainly in terms of search and rescue here in the province, but particularly in terms of the humanitarian response that we looked for [from] them on the search for that young man from Labrador."
The premier said in May it has been a "frustrating" four months trying to get answers from MacKay and getting him to take responsibility for "poor judgment in decision-making and a timely response."
Dunderdale also expressed concern over how EI reform could impact people in the province.
The federal loan guarantee for the proposed Muskrat Falls hydro project has yet to be finalized.
The Harper Conservatives made that pledge — a guarantee, or equivalent financial aid — during the 2011 federal election .
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