"In the 21st century, such attacks against the civilian population are unthinkable and abhorrent," Czech Foreign Minister Jan Lipavsky said on Twitter.
"We must not overlook it. We stand for the punishment of all war criminals," he added.
"I call for the speedy establishment of a special international tribunal that will prosecute the crime of aggression," Lipavsky said.
Investigators said some bodies in the graves found near the eastern Ukrainian city of Izyum had hands tied behind their backs. They also found the bodies of children.
The Czech Republic, a former communist country and now EU and NATO member, has received around 400,000 refugees from Ukraine and provided military aid worth some $150 million to the country invaded by Russia on February 24.
