Obama, currently visiting Malaysia, was speaking during a press meet with Malaysian Prime Minister Najib Razak in Kuala Lumpur.
In Washington, State Department spokesman John Kirby also said the US is closely following reports of the ongoing hostage situation involving shooters at the hotel in Mali's capital Bamako.
"We are aware US citizens might be present at the hotel. The US Embassy in Bamako is working to verify the information. Given the fluidity of the situation, we do not have any additional details to share at this time," Kirby said.
Obama said, "We have developed a very strong relationship around counter-terrorism. Malaysia, like Indonesia, are majority Muslim countries that represent tolerance and peace and as a consequence its voice is critical in the debate taking place internationally around terrorism".
"Malaysia is part of the coalition to fight IS (Islamic State) and has been particularly helpful on issues like countering the destructive and perverse narrative that's developed," he said.
"Malaysia's willingness to host a center that uses all the tools of social media and scholars and clerics to counter this violent narrative is extremely useful," added Obama.
"This region is not immune from threats of violent extremism and there are groups that have announced they are aligned with IS. Malaysia's government is very clear we are against IS, against the ideology. It is evil. It is against Islam. It is a perversion of Islam, and they do not represent us," Najib said.
"We will work very closely together with the United States and like-minded countries to make this region safer and combat any form of violent extremism. We have also agreed to make Malaysia a long-term center for counter messaging. In fighting violent extremism, it's not just only a military solution that's required," Najib said.
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