"Slovakia can now say that we have met our commitment to the EU," Economy Minister Lubomir Jahnatek told reporters gathered at the plant.
"The VI unit started to lower its output shortly after the noon and will be definitely shut down at 7:00 p.m," (1800 GMT) he added.
But in November, Prime Minister Robert Fico said the VI nuclear block might be reopened later to offset the fallout of the global financial crisis.
"The VI nuclear block should be shut down using such technology that "in case of a possible future crisis, when Europe may need help, we should be able to revive the plant," he said.
After the European Union said the reactors were unsafe, Slovakia closed the first nuclear block at Jaslovske Bohunice, about 50 kilometres northeast of Bratislava, at the end of 2006.
It agreed to switch off the second bloc of the Soviet-designed reactor at the end of December 2008, before joining the EU in 2004.
But it has always argued that experts say both blocks were safe and could have continued to operate until 2020 or 2025.