Configurable using the Quartus II Pin Planner.
 
The setting method is shown below.
1. Select Assignments ⇒ Pin Planner from the Quartus II menu bar.
2. Select View Show Show I/O Banks from the menu bar of the Pin Planner window to display the View display.
Switches for each bank.
3. Right-click the IOBank you want to configure ⇒ select I/O Bank Properties….
4. In the I/O Bank Properties window, in the I/O Bank VCCIO: field, select the desired voltage from the pull-down menu.
Select and click OK.

After changing the settings, compile (Fitter) and this setting will be reflected. * Be sure to check the compile report to see if the VCCIO of the corresponding bank is the set value.