In the provinces of Nova Scotia, New Brunswick and Prince Edward Island the stations opened at 8:30 a.m.(1130 GMT), and a half hour earlier in the island province of Newfoundland.
Polling showed Justin Trudeau's Liberals with a strong lead on the eve of the vote after a gruelling 11-week campaign.
The 43-year-old the son of former prime minister Pierre Trudeau is hoping to unseat Harper, who is seeking his fourth mandate, after nine years of Tory rule.
According to the Nanos poll, the Liberals have the support of 38.2 percent of Canadians, versus 30.1 for the Conservatives and 21.2 percent for the New Democratic Party, lead by Thomas Mulcair.
Up to 26.4 million electors are expected to vote in 338 electoral districts. Some 3.6 million already cast a ballot in advance voting a week ago, and the turnout Monday is expected to be high.
Polling stations are scheduled to open gradually in other provinces in six time zones throughout the day.
They will close in central Canada at 9:30 pm local time, and a half hour later in westernmost Canada, including Vancouver.