Witnesses reported hearing gunfire, mortars and rocket-propelled grenades being fired from midnight on Monday until dawn on Tuesday.
Supporters of the Future movement, which is a member of the parliamentary majority, and the opposition Hezbollah fought in the same two villages earlier this month.
The violence comes in spite of a deal reached in Qatar on May 21 that led to the election of Michel Sleiman, the head of the Lebanese army, as president.
The agreement between the majority and opposition was reached after an 18-month political deadlock.
However, the majority and the Hezbollah-led opposition have so far failed to agree on the formation a new national unity government.
Future movement officials earlier this month said they may withdraw from talks on the cabinet line-up, citing the violence.
"The clashes are continuing because both sides are acting irresponsibly," the army official said after the latest violence.
"If we don't reach a complete solution, there will always be potential for repeated clashes."
Zeina Khodr, Al Jazeera's correspondent in Lebanon, said: "No one can independently confirm what or who triggered the clashes but they were not the first in this area.
"The violence serves as a reminder of the dangers if reconciliation is not forged.