Water was seeping into the turbine station there, but plant officials say it poses no safety risk because that building contains no nuclear material.
Workers at a second nuclear plant near Brownville, Nebraska, have put up a 10-foot wall to keep water out, but so far the plant continues to operate normally.
Nuclear Regulatory Commission Chairman Gregory Jaczko visited both Fort Calhoun and Cooper nuclear power plants this week to see how the utilities that run them are coping with the flooding. Both plants sit on the river.
Jaczko said the Army Corps of Engineers doesn't expect the river to rise enough to cause additional significant problems at either of the nuclear plants in Nebraska.
"Bottom line, it looks like the levels are going to be at a place where the plant should be able to deal with it," Jaczko said.
Flooding remains a concern all along the Missouri because of massive amounts of water the U.S. Army Corps of Engineers has released from upstream reservoirs. The river is expected to rise as much as 5 to 7 feet above flood stage in much of Nebraska and Iowa and as much as 10 feet over flood stage in parts of Missouri.
The Associated Press contributed to this report.
