"For many, this month is an opportunity to focus on reflection and spiritual growth, forgiveness, patience and resilience, compassion for those less fortunate, and unity across communities," he said in the message issued on Sunday evening.
"Here in the US, we are blessed with Muslim communities as diverse as our nation itself. There are those whose heritage can be traced back to the very beginning of our nation, as well as those who have only just arrived," he said, noting that their numbers include "doctors, lawyers, artists, teachers, scientists, community organisers, public servants, and military members," CBS News reported
Then, in pointed contrast to the Republican Party's presumptive presidential nominee Donald Trump's call to temporarily ban Muslims from entering the country, the president stated: "I stand firmly with Muslim American communities in rejection of the voices that seek to divide us or limit our religious freedoms or civil rights."
"We will continue to welcome immigrants and refugees into our nation, including those who are Muslim," he added.
Trump stood by his proposed ban in an interview on Sunday with CBS News' "Face The Nation".
"I'm not backing down. We have to do something. We have a problem in this country. We have a radical Islamic terrorism problem in this country, and, by the way, throughout the world, throughout the world. It's a problem. And it's a temporary ban. I'm not talking permanent. It's a temporary ban. We have to find out what is going on," said Trump.
As he has in past years, the president said he will invite a number of Muslim Americans to the White House for Eid celebrations, the holiday marking the conclusion of Ramadan around the first week of July.