"Low voter participation will be a problem for our democracy and could lead to a debate on legitimacy," Muammer Aydin told the mass-circulation Sabah newspaper.
Some 42.6 million voters are registered to cast their "yes" or "no" ballots in 134,000 polling stations on the constitutional reform package that provides for a two-round popular vote, instead of a parliamentary vote, to elect the head of state.
The reforms also allow for presidents to serve two five-year terms instead of the current single, seven-year term, and set general elections for every four years instead of the current five.
Polling begins at 7:00 am (0400 GMT) and continues until 5:00 pm (1400 GMT).
Observers say the ruling Justice and Development Party (AKP), which drew up the reform package, is likely to garner the necessary support in Sunday's vote, which comes less than three months after a general election that gave the party a second five-year term in power.
With no public debate on the issue, media interviews with people on the street show that Turks have very little knowledge on the actual content of the reforms and that some do not even know that a referendum is taking place.