Checks will now be performed on 20 instead of 14 border crossing points as of Saturday, including those on minor roads, said the ministry.
"It is an expansion of a measure now in force," said Interior Minister Milan Chovanec, stressing this was not a reintroduction of regular border checks.
The Czech Republic is part of Europe's Schengen passport-free travel zone, which has come under intense pressure as the EU struggles to cope with an unprecedented influx of refugees and migrants.
Some 200 police officers were deployed to assist with extra checks in mid-September. The ministry did not say how many more would be needed for the new measure.
The interior ministry also said it was considering cancelling some international trains should Austria close its borders with all neighbours except the Czech Republic to stem the passage of refugees heading to Germany.
Unlike EU neighbours Austria and Hungary, the Czech Republic, Poland and Slovakia have so far seen few refugees and migrants seeking to transit through their territories to Germany and other western European countries in recent months.