"Three soldiers were killed and three wounded soldiers were admitted to the hospital," said Al-Jala hospital spokeswoman Fadia al-Barghathi.
A security source indicated that the fighting erupted east of the city.
"These victims fell in clashes in the Sidi Khalifa district between the army and an armed group that was trying to enter the city from the east," the source said, adding that the group's allegiance was unknown.
Earlier today, witnesses said gunmen inside the city killed a soldier on the final day of a three-day strike in protest over militias.
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"The soldier died after being shot in the head," said a medic at Benghazi's Al-Jala hospital.
Witnesses said the second soldier escaped unharmed.
The strike was sparked by a shootout on Monday between a jihadist group and the army left seven people dead and 50 wounded.
Today's killings come a day after three soldiers were shot dead and the bodies of two more were found in the nearby town of Derna.
Libya has seen mounting unrest since the toppling of long-time dictator Moamer Kadhafi in 2011 by a ragtag assortment of rebel brigades, many of which have since been transformed into militias that defy the weak central government.