The 44-year-old multiple Grammy and Juno award winner wrote a letter that was posted on the Web site of the People for the Ethical Treatment of Animals, the Toronto Star reported.
The annual hunt began Tuesday in the Gulf of St. Lawrence and expands Thursday off Newfoundland's northeastern coast.
McLachlan alleged Harper's Conservatives tolerate the hunt for political reasons.
"It seems that the only reason why the federal government defends the dying seal-slaughter industry is to control the parliamentary swing seats in Newfoundland and Labrador," McLachlan wrote.
Calling the seal hunt "about as lucrative as an eight-track tape factory," she said Harper should treat the hunt as other dying industries were.
"The sealers -- like tobacco farmers and asbestos miners -- need leaders to devise a practical exit strategy for them, not waste millions more in hopeless World Trade Organization challenges or paying to stockpile pelts when buyers already have seal pets going back several years," the letter said.
There was no immediate response from Harper's office, the Star said.