Instead, the Conservatives will once again be forced to rely on opposition support to pass budgets and legislation - as it has had to since a 2006 election victory.
Harper sought to put a good face on the results Wednesday, pointing to an increased number of seats and pledging cooperation.
"We have shown that minority government can work and at this time of global economic instability we owe it to Canadians to demonstrate this once again," Harper said. "We hold out a hand to all members of all parties asking them to join together to protect the economy and weather this world financial crisis."
With nearly all the returns in, Canada's election agency reported on its Web site that the Conservatives had won or was leading in races for 143 of Parliament's 308 seats, an improvement over the 127 seats the party had in the previous Parliament.
The Conservative Party needed to win 155 seats to govern on its own.
The Liberal Party, long Canada's top party, suffered a severe drubbing, dropping to 76 seats from 95 in the previous Parliament, according to the election agency. Bloc Quebecois won 50 seats, the New Democrats 37 and independent candidates 2.
Liberal Party leader Stephane Dion, in his concession to Harper, offered his "full cooperation in these difficult economic times."
The party winning the most seats generally forms the government, with its leader becoming prime minister. The opposition parties could unite and topple Harper if they won enough seats for a majority, but analysts said that was unlikely because the parties have no tradition of forming such coalitions.
The opposition Liberals have typically been the party in power, forming the government for most of Canada's 141 years. But the left-of-center vote was divided among four parties, giving an edge to the Conservatives.
Dion's campaign was hindered by his unpopular plan to tax all fossil fuels except gasoline and by perceptions he is a weak leader. A former professor from French-speaking Quebec, Dion also suffered in other regions because he frequently mangles English grammar and his accent makes him hard to understand.
Dion said Canadians have asked him to be their official opposition leader, a signal that he's not ready to step down at this point.
If Dion was ousted as leader after a loss, he would be just the second Liberal leader to fail to become Canada's prime minister. The only other was Edward Blake, who led the party to defeat in the 1882 and 1887 elections.
Many Canadians complained Harper was slow to react as the global credit crisis worsened. He hurt himself by saying during a debate that Canadians were not concerned about jobs or mortgages. A few days later, he said stocks were cheap - just before Canada's main stock exchange had its worst week in almost 70 years.
Harper later said he knows Canadians are worried and stressed that Canada's economic and fiscal performance contrasts to the more dire situation in the United States.
Voter turnout Tuesday about 59 percent, the lowest in Canadian history. It was unclear how much stringent new proof-of-identity requirements affected the turnout.