Opponents say he wants to halt NATO membership altogether.
Pavilionis, the former dean of Vilnius University, says fellow politicians and government officials are afraid of democracy.
In the back and forth over the last months on Pavilionis' plans to hold a poll on NATO, things recently turned nasty, with conservative MP Vytautas Landsbergis playing his classical gambit, calling an opponent who wins an intellectual argument a KGB agent.
Pavilionis says NATO membership must be subject to referendum because of the monumental changes it would make in the life of the nation. The Lithuanian constitution requires public referenda on all issues of major importance.
Past referenda in independent Lithuania have been on the constitution itself, adopted in 1992, and the introduction of the office of president (to take over from the de facto leadership of the parliamentary chairman, then Landsbergis).
After Pavilionis broached the idea a few months ago, fellow MPs began to talk about introducing two classes of referenda in Lithuania: binding and consulting, to consult with the public but not necessarily listen to what it has to say.
Roundly condemned by the majority of parliamentarians even in his own faction, Pavilionis was left with the option of dropping the idea or collecting the hundreds of thousands of signatures needed to bring it to vote. Last week Pavilionis and a group of 16, including MPs and public figures, chose to take it to the people.
"According to our data, 70 percent of citizens are in favor of holding a referendum on Lithuanian entry to NATO," they said, calling the measure "a necessary condition" for showing Lithuania is democratic and that the people have the final say in the course of state.
Naysayers call the referendum unnecessary and a waste of money. They rightly argue NATO itself doesn't require a referendum, only ratification in Parliament.
Pavilionis' group proposes holding the referendum along with the presidential election in December to save costs.
When cornered, opponents admit they're afraid voters might reject NATO membership, meaning Lithuania wasted 10 years and lots of money to join. A few years ago responsible parties in the Lithuanian Foreign Ministry were pouring cold water on the idea of an EU membership referendum, before news had reached Lithuania that all new EU members hold public referenda before joining.
While referenda may not be the norm in the mostly Cold War-membership roster in NATO, Finland has recently been talking about a referendum on joining the military organization, and it seems likely in future rounds of expansion.
Even before independence, Lithuanian state policy has been marked by drives to achieve concrete goals, first independence and now NATO and EU membership. The thinking has been: come what may, everything will take care of itself after these fundamental goals have been reached.
That has allowed politicians of the day to ignore problems at hand, to postpone what in a normal situation would be their duties as politicians to reach higher goals in the future. It has also meant the emergence of an elite acting in opposition to the unknowing public, worried by mundane matters like paychecks, taxes and education.
The problem is that the Cold War is over, and the war-footing mentality underlying this style of governance is becoming a hard sell. Like it or not, NATO has become a political as well as a military organization, with activities ranging from environmental protection to fire fighting, and search and rescue.
That means referenda are in order for new members if NATO is to continue to proffer itself as a bloc of democratic and free nations aligned for mutual self-defense.
In Lithuania's case, there's no way around it. Article 9 of the constitution demands it: All the most important issues in the life of the nation are solved by referendum.
The law is clear.