The Conservatives, now with a majority at Westminster, have pledged to replace the Act with a British Bill of Rights.
They want to give UK courts and Parliament the "final say" on human rights issues rather than Strasbourg.
Asked about the impact of such a change on Wales, Mr Jones told assembly members: "It would make us look like a Banana republic, frankly."
The Human Rights Act came into force in 2000, bringing the rights contained in the European Convention on Human Rights into UK law.
Critics say the Act has led to "perverse" judgements, including a ruling that found the UK's blanket ban on prisoners voting was unlawful.
But during Tuesday's First Minister's Questions, Mr Jones said: "Most countries in Europe including Russia are signatories, are members of the European Convention.
"The European Convention was drafted by British lawyers; it's a British invention, and there's a complete lack of understanding of history in Whitehall at the moment," Mr Jones added.
Under the Conservatives' plan, the European Courts would not be able to require the UK to change British laws, with its judgements being treated as "advisory" rather than binding.
Instead, the UK's Supreme Court would be "the ultimate arbiter" on human rights matters.
Welsh Liberal Democrat leader Kirsty Williams accused Conservative ministers of wanting to "put us in the same category as Kazakhstan in terms of how we view human rights".
"Liberal Democrats stopped the Tories scrapping the Human Rights Act and we are determined to keep fighting these plans," she said.
The European Convention created basic human rights and freedoms for every citizen in Europe.
They include the rights to life, liberty and security, a fair trial, respect for private life, and freedom of expression.
A Ministry of Justice spokesman said: "The Government was elected with a manifesto commitment to replace the Human Rights Act with a British Bill of Rights.
"Ministers will be discussing their plans on this and making announcements in due course."

The closure of Imperial Tobacco's Horizon factory in Nottingham was announced two years ago and will lead to over 500 job losses.
Most of the staff will leave next week, with 70 staying on for 18 months as part of the "decommissioning process".
The site's closure has been blamed partly on attitudes to smoking.
Chris Needham, regional organiser for the GMB trade union, said at its height, the firm employed 7,000 staff and made 52 billion cigarettes each year.
Mr Needham said operations would move to Poland and Germany, which will increase profits by Â£320m.
"We're talking about generations that have been manufacturing in Nottingham since 1860," he said.
"The Horizon factory has been part of Imperial Tobacco, worldwide, producing profits in the billions."
Mr Needham said 16 to 17 billion cigarettes - or "sticks" as they are known by staff - were produced last year.
"The issue is about quantities," he said. "And the stigma of smoking has been one of the major factors.
"They [the company] are moving to the Asian markets where the stigma is not as great. Iraq, Syria, Russia, China - these are places I'm sure will be targeted by Imperial Tobacco."
Janet May Dangerfield, who worked at the firm in the 1970s after she left school at the age of 15, expressed her sadness at the firm's demise.
"I'm very shocked and sad because I always thought that would always be there," she said.
"I can remember my first day. I was very nervous but straight away, all the older ones - I think they were called the 'front girls' and 'second front girls' - took me under their wing."
When she moved into the "vast" Horizon factory, Mrs Dangerfield said the size of the site made her and other employees look like "little mice".
Bosses at the factory previously blamed falling sales and an increase in the illegal tobacco trade for their decision to move out of the UK.
History professor John Beckett, from the University of Nottingham, said the business was actually a "major contributor" to the funding required for the city's Queen's Medical Centre.
"It's been in decline ever since the first reports in the 1950s that smoking was bad for your health," he said.
"Gradually, much of the production has been moved abroad, much of it into countries where it's cheaper such as Poland... and the demand here has almost collapsed."
A company spokesman confirmed the plans for closure, but did not offer anyone to comment on the latest developments.
Scrapping the Human Rights Act would "make us look like a banana republic", First Minister Carwyn Jones has warned.
[NEXT_CONCEPT]
The last pack of English-made cigarettes has rolled off the production line as the country's only tobacco factory prepares to shut.