The human rights pressure group has accused Mr Howard of portraying asylum-seekers as a threat to national security and of sponsoring policies as divisive as Zimbabwean President Robert Mugabe's regime.
In a report released on Wednesday, it also criticised Australia's role in the war on terror and its treatment of female victims of violence.
Amnesty secretary-general Irene Khan said the fear generated by leaders such as Mr Howard "thrives on myopic and cowardly leadership".
Ms Khan lumped Mr Howard in with Mr Mugabe, US President George W Bush and Sudan's President Omar al-Bashir in a paragraph about leaders who used fear to suit their political agenda.
In statement today, Mr Howard rejected the way Australia was characterised in the Amnesty report.
"The report's entry on Australia contains a string of assertions, unsupported by evidence and devoid of context," he said.
"The report's treatment of Australia amounts to little more than a shoddy caricature.
"Nowhere is the report's political agenda clearer than the paragraph in its foreword which seeks to bracket Australian and US policies with the horrendous human rights situation in Darfur and Robert Mugabe's disastrous misrule in Zimbabwe."
Ms Khan stood by her comments today, accusing the Howard government of having an "appalling" domestic human rights record regarding its treatment of asylum seekers and indigenous people.
These failures had undermined its good work overseas, she told ABC Radio.
Mr Howard said he respected Amnesty, but its current leadership had lost sight of the need for balance or rigour.
"I believe many Australians will be as offended by this report as I am," he said.
"My government makes no apology for taking appropriate, balanced steps to protect the Australian public from the very real threat of terrorism and to protect our borders."