The Morava River, in the Czech Republic, has burst through flood barriers in the town of Olomouc, 250 km south-east of Prague, causing many residents to evacuate, deputy mayor Martin Novotny said.
A total of 2,500 people may have to be evacuated if water levels continue to rise, he added.
The governor of the south-east region of South Moravian, Stanislav Juranek, ordered the evacuation of nearly 4,000 people from three small towns near the border with Austria, all threatened by water from the Dyje and Jevisovka rivers, CTK reported.
In the north, authorities ordered a mandatory evacuation from Hrensko, on the border with Germany, Usti region spokeswoman Sarka Roudnicka said.
The Elbe River continued its dramatic rise, reaching 8.4 metres in the town of Usti nad Labem, up from the usual 2 metres, but not a record breaker – in 2002, when floods killed at least 16 people and caused nearly 2.5 billion euros ($A4.27 billion) in damage, the Elbe reached 12 metres in Usti nad Labem.
"No tragic events are immediately threatening us, but I'm afraid we do not have things under control yet," Prime Minister Jiri Paroubek said during a live TV debate.
"Much will depend on the weather," he added.
A pensioner was found dead in the Trebovka river, in the east of the country, raising the death toll to six, the news agency CTK said.
Slovakia
Another two people have lost their lives in neighbouring Slovakia, where the river levels remained critical although the risk appeared to be easing.
A state of emergency was declared Saturday at Trtice in the south-west of the country after the Cierna Voda reached a dangerous level.
Germany
In the German town of Dresden, which also lies along the Elbe, flood waters were rising more slowly than predicted, reaching only 7.4 metres - below the 8-metre mark which would endanger the historic inner city district.
Fire-fighters, soldiers and volunteers continued to fill and stack sandbags in an effort to reinforce dams and prevent the water from lapping into homes.
Still, 100 people were forced to leave their homes, a spokeswoman for the city said.
Hungary
Close to 400 people had to be evacuated from 45 towns across Hungary because of the flooding.
In the capital Budapest, 33 people were moved out of their homes in low-lying areas along the Danube River, which was expected to peak on Tuesday.
Volunteers were filling sand bags on Margaret Island, a popular recreation spot in the middle of the Danube, in an attempt to guard against the rising water.
Budapest's mayor has urged the government to declare a state of emergency for those parts of the city most threatened by the Danube and ban traffic on the river.
Prime Minister Ferenc Gyurcsany said the situation was “dramatic", but it was not necessary to declare a national emergency, yet.
Austria
In Austria, the Danube remained closed to ship traffic, with levels nearly half a metre above those deemed safe.
Although many of the rivers in the north remain at a critical situation, no residents were forced to leave their homes.