"Nobody should have to worry about their security when gathering with their fellow believers. No one should have to fear for their safety when they go to prayer," Obama said at the White House, a day after the shooting in Kansas.
The president said the shooting was particularly tragic because it came as Jews were preparing to celebrate Passover and Christians were marking Palm Sunday.
He said that the US government would provide whatever assistance necessary to help the affected community, as synagogues and other religious sites hike security measures.
"We have to keep coming together across faiths to combat the ignorance and intolerance, including anti-Semitism, that can lead to hatred and to violence."
Alleged gunman Frazier Glenn Cross, now in custody, was a former Ku Klux Klan leader and had a history of anti-Semitism, said the Southern Poverty Law Center (SPLC), which tracks hate groups.
He reportedly yelled "Heil Hitler" as police escorted him away in Kansas City yesterday.