"Weather is the biggest concern for people. Everybody is worried whether it will rain," Gintaras Grušas told reporters in Vilnius on Thursday.
"Let's have hope and pray for a nice weather, but let's not be afraid (of bad weather)," he added.
The pontiff will arrive in Vilnius on Saturday and will travel to Kaunas on Sunday.
Temperatures in the capital are forecast to drop to 16 degrees Celsius on Saturday, with rain expected in the morning and some occasional showers likely in the afternoon.
Similar weather conditions are forecast for Kaunas on Sunday.
"The forecast for temperatures is unlikely to change, but it may rain even longer than we expect now," forecaster Edita Gečaitė told BNS.
Following his visit to Lithuania, the pope will travel on to Latvia and Estonia.