"This is the longest blockade since the year 2000," Roland Egger, spokesman for the "Atomkraftfrei Leben" (life without nuclear power) movement told AFP.
The blockade, which began at 2:00 pm (1300 GMT) at the Wullowitz-Dolni Dvoriste border crossing, was to last six hours and authorities were expecting up to 500 protesters by 8:00 pm.
The demonstrators want the Austrian government to voice an official protest against the Czech authorities' recent validation of the Temelin plant.
They say the validation violates the Melk agreement signed by the two countries in 2000, as security measures required by the document have not been met.
The protesters, whose gathering was sanctioned by the Austrian authorities, gave out yellow balloons, stickers and mulled wine to nearby residents who had turned up at the border crossing, which was decorated with banners reading "Stop Temelin".
The neighbouring border crossing at Gmuend was also blocked for about an hour by about thirty protesters on Sunday afternoon. The demonstrators said they were prepared to organise as many blockades as necessary until their demands were met.
Built in 1987 according to an original Soviet design with Western security systems added on, the Temelin plant, about 60 kilometres (40 miles) north of the Czech-Austrian border, was opened in 2000.
But since then, it has been plagued by a series of problems, especially on its second unit, which have forced the plant to shut down its two reactors on several occasions.
Non-nuclear Austria has questioned the safety of the power plant but the Czech authorities say it is in line with European regulations.