Zardari made the remarks while addressing the concluding session of a national conference on inter-faith harmony at the presidency.
He called for unity and harmony among the people to address the challenges of extremism and terrorism.
He said he had been pleading with the world community that the way the issue of terrorism was currently being addressed would not lead to success.
"We believe in tolerant Islam and have to counter those who believe in hate, with peaceful efforts," he said.
The banned Tehrik-e-Taliban has said it is willing to hold a dialogue with the government but will not disarm.
Interior Minister Rehman Malik recently called on the Taliban to prove that it is sincere about talks by announcing a month-long truce.
The Taliban rejected the demand.
During his address at the conference with the theme of "Living together with diversity � Interfaith and inter-cultural dialogue", Zardari referred to the fight against terror in Afghanistan and said more than three decades of war could not bring peace to the neighbouring country.
There was a time when no one in Pakistan could think of a person blowing himself up as a suicide bomber as Islam was against suicide, he said.
People lived in peace and harmony and there were no sectarian issues but global politics changed the situation and religion was used as a weapon of war, he said.
The session was attended by Pakistan People's Party chairman Bilawal Bhutto Zardari, Advisor to the Prime Minister on National Harmony Paul Bhatti and retired judge Rana Bhagwan Das, who said the challenge of terrorism could be addressed through unity and tolerance.
The conference also recommended the encouragement of inter-faith dialogue and steps that should be taken by the international community to address the root causes of terrorism.
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