The Associated Press agency reported on Tuesday that "the warning came as a growing number of deaths was reported among Czech tourists in the Balkan country".
To date, 14 Czech citizens have died this summer in Croatia and another two are currently missing, the ministry reported.
The AP quoted the ministry as saying that some of the victims " underestimated actual weather conditions".
The ministry advises Czechs "to strictly follow instructions by local Croatian authorities".
In the latest incident, which occurred over the weekend, a 16-year-old Czech tourist was killed by lightening while sailing in a small rubber boat 200 metres from the coast near the town of Biograd.
The AP added that "Croatia's Adriatic coast is popular destination for Czechs in summer and some 800,000 of them are estimated to spend their vacation there this year".