The prime minister signed a book of condolences for Havel, former president of the Czech Republic and Czechoslovakia, who died on the weekend.
Havel was the leader of his country's anti-communist Velvet Revolution in 1989. The one-time dissident playwright died Sunday at 75.
"I want to express to all Czechs the condolences of all Canadians on the passing of one of the truly great men of our age," Harper wrote Wednesday at the Czech Republic's Ottawa embassy.
"While this is a sad event we all know that as long as freedom endures, the spirit of Vaclav Havel lives on."
Gov. Gen. David Johnston will attend Havel's state funeral Friday at St. Vitus' Cathedral at the historic Prague Castle. He said Havel was a force for liberty, human dignity and democracy.
Among Havel's many international honours was his honorary Companion of the Order of Canada.
"As a peaceful leader against tyranny, he fought for freedom and inspired his fellow citizens and millions across the continent. His spirit and dedication led a generation to hope and prosperity," Johnston said in a statement.
"He embodied the values and beliefs Canadians hold so dear. On behalf of all Canadians, it is an honour to pay tribute to one of the greatest statesman of the 20th century."
The casket bearing Havel's body was being transported from the Prague Crossroads, the former church Havel turned into a cultural centre, to Prague Castle, the seat of the presidency.
Thousands of Czechs joined Havel's widow, friends and relatives, who lined the sombre route of the black car bearing his body. Many greeted its passing with applause.
One onlooker called it a "last opportunity to say goodbye."
Havel paid a memorable visit to Ottawa in 1999, bringing hundreds of Canada's politicians to their feet in a stirring speech to Parliament.
He talked about democracy, human rights and the war in Kosovo and made an idealistic prediction of the world in the future.
"The idol of state sovereignty must inevitably dissolve in a world that connects people — regardless of borders — through millions of links of integration ranging from trade, finance and property, up to information; links that impart a variety of universal notions and cultural patterns," Havel said between frequent interruptions of applause.
"Furthermore, it is a world in which danger to some has an immediate bearing on all; in which ... our fates are merged together into one single destiny."
Havel also touched on human rights, saying "human liberties constitute a higher value than state sovereignty."
"The provisions that protect the unique human being should take precedence over the provisions that protect the state," said the man who went from prisoner to president in 1989, the year the Berlin Wall fell.
The speech prompted a tribute from then-prime minister Jean Chretien, who noted Havel's personal journey and that of his country "speak to how far the cause of freedom and human rights have come in Europe."