"We will submit a new version of the law, the toughest ever here -- a complete ban on smoking in restaurants," the Lidove noviny broadsheet quoted deputy health minister Martin Plisek as saying.
Under the current law, restaurants are free to decide whether to permit smoking inside.
Slapping hefty fines on offenders, the new proposal would also ban smoking in beer gardens with a roof but tolerate smoking in roofless ones.
The CTK news agency quoted a May survey by Prague-based Charles University, which showed 78 percent of Czechs were in favour of a complete ban on smoking.
Plisek said the ban could take effect in August 2013.
The Czech Republic ratified the World Health Organization's convention on tobacco control in June as the last EU member country, after eight years of delays.
In the Czech Republic, an ex-communist country of 10.5 million which joined the EU in 2004, three in ten people older than 15 years are smokers, according to a recently published EU survey.
Among Czechs aged 15-18 years, smokers make up 40 percent.