"The Czech Republic is boosting measures on its border with Austria. Further steps will be determined according to the number of refugees heading to the Czech Republic," Interior Minister Milan Chovanec told public Czech Television.
Germany's decision to reinstate controls on its border with Austria meant the Czech Republic is "now the only bypass" for refugees, he added.
"We are doing our best to send a clear signal that we will observe the European law on our borders... And boost the performance of our people on the border so that we would be able to return migrants to the neighbouring country," said Chovanec.
"The EU was not able to thoroughly observe its own rules when handling the migrant crisis and efficiently protect the outer border of the Schengen area," said Sobotka.
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"So now it is necessary to take operational steps to boost the security of individual countries and contain the inflow of refugees."
He said the EU should better regulate the inflow of migrants on its outer borders and "ensure dignified conditions for asylum seekers and distinguish war refugees from economic migrants".
Like other ex-Communist EU members in central Europe including Hungary, Poland and Slovakia, the Czech Republic has vehemently opposed refugee redistribution under a compulsory quota system drawn up by the European Commission and pushed by EU powerhouse Germany.
Sobotka said earlier today the quota system "won't work" as migrants will want to continue to Germany or Sweden instead of staying in the poorer central European countries.