Atheists in Malaysia should be “hunted down” as they violate the constitution, a government minister in the increasingly fundamentalist Muslim-majority nation has said.

Shahidan Kassim, who serves in the Prime Minister’s inner circle, called on Islamic scholars to re-educate non-believers.

Apostasy is not a federal crime in Malaysia, but critics say the country’s increasingly conservative trajectory is threatening religious freedoms.

“The [Federal Constitution] does not mention atheists. It goes against the Constitution and human rights,” Mr Kassim said during a press conference.

“I suggest that we hunt them down vehemently and we ask for help to identify these groups.”

The MP for Arau, a town in the far north of Malaysia close to the border with Thailand, said atheists were “misled” and claimed they “don’t want to be atheists but it happens because of the lack of religious education”.

Mr Kassim called on “all muftis [Muslim religious scholars]” to “return them to the faith”.

It comes as the Malaysian government ordered an investigation into an international atheist organisation that is operating in the country.

A photo of a meeting of the Kuala Lumpur chapter of Atheist Republic sparked uproar among some Muslims and lead to death threats against the group on social media.

Malaysia's deputy minister in charge of religious affairs, Asyraf Wajdi Dusuki, said on Monday he had instructed the Federal Territories Islamic Religious Department to investigate the Atheist Republic chapter to see if any Muslims were involved.

"We need to determine whether any Muslims attended the gathering, and whether they are involved in spreading such views, which can jeopardise the aqidah [faith] of Muslims," he told Reuters.

Ex-Muslims in the group would be sent for counselling, while attempts to spread atheist ideas could be prosecuted under existing laws, Asyraf said.

"We need to use the soft approach with (apostates). Perhaps they are ignorant of the true Islam, so we need to engage them and educate them on the right teachings," he said.

Atheist Republic's founder, Armin Navabi, said the group's gatherings caused no harm to the public and were not considered a threat in other countries.

"They [atheists] are treated like criminals. They are just hanging out and meeting other atheists. Who are they harming?!" he said in a post on his Facebook account.

Malaysian states, which have their own laws governing Islamic affairs, do not allow Muslims to formally renounce Islam, preferring instead to send them for counselling, or fining or jailing them.

The country's apostasy laws have left many former Muslims in legal limbo, as they are not allowed to register their new religious affiliations or legally marry non-Muslims.

In 2007, Lina Joy, a Malaysian convert to Christianity, lost a high-profile legal battle to have the word "Islam" removed from her identity card. In delivering judgment in that case, the Federal Court's chief justice said the issue was related to Islamic law, and civil courts could not intervene.