However, environmental groups criticise the regulators for not putting restrictions on the mineral, according to Lexington Herald-Leader.
The state Division of Water stalled for two years before releasing the information, the groups said.
"What makes us the maddest is that the division has had this information for a while now," said Judith Petersen of the Kentucky Waterways Alliance.
The main concern with the levels found in Eastern Kentucky is the effect on fish and wildlife, Ms Petersen said. But in higher doses, selenium can be toxic to humans.
State officials said the suggestion that they withheld information is "inaccurate and false".
But Peter Goodman, assistant director of the state Division of Water, said an employee erred when he repeatedly denied an environmental group's request for selenium test results through the Open Record Act.
The groups – the Sierra Club, the Appalachian Center for the Economy and the Environment and the waterways group – said the state surveyed 13 sites in the region in 2007.
At one mining site and one road cut, it found that water downstream exceeded state water quality standards. Other mining sites showed elevated levels.
At three mining sites, the groups said, tests of fish tissue exceeded the federal Environmental Protection Agency's recommendations for the mineral.
In five other areas, the levels in fish were high enough to be harmful to the fish.
Margaret Janes, with the Appalachian Center for the Economy and the Environment, told Lexington Herald-Leader that the fish tissue results were more telling than the water tests. Selenium accumulates in fish as does mercury, she said, showing chronic exposure.
Selenium is naturally occurring, and in small amounts it is necessary for good health.
But coal mining releases high levels into the environment. Ash left after coal is burned to produce electricity also contains high levels.
After studies in 2002 found selenium in West Virginia, limits – not yet enforced – were put on the amount allowed.
Mr Goodman said the Division of Water became concerned about selenium in Kentucky after seeing the West Virginia results and set in motion the process that led to the testing here.
In Kentucky, the state released a new Clean Water Act general permit for mines in July without selenium restrictions.
Ms Petersen said the state needs "to act now to set limits in permits and require regular monitoring to protect people and wildlife in Eastern Kentucky."
Mr Goodman said that a general permit application has to include selenium monitoring results from that mine or an adjacent mine. If selenium shows up at significant levels, the mine operator has to apply for an individual permit, which is stricter.
Karen Wilson, the chief of staff for the state Energy and Environment Cabinet, said West Virginia appears to have more widespread selenium problems than Kentucky but added that "selenium is a constituent of concern that warrants being addressed further in Kentucky."
Mr Goodman said the Kentucky study that caused the current controversy is not yet complete.
The Division of Water's Randy Payne received reports about selenium near Kentucky mines a year ago, Mr Goodman said, but thought they were not subject to the Open Records Law because he had not completed quality assurance on the data until three weeks ago.
A previous attorney for the division had taken that position, Mr Goodman said, but the current attorney does not.
"In that regard, we may have made a mistake, but it was not a conspiratorial mistake," Mr Goodman told Lexington Herald-Leader.
Dangerous Levels of Selenium in Water, Fish in KY
KENTUCKY, US - State regulators have found dangerously high levels of selenium in water and fish near coal mines in Eastern Kentucky.