"We have lost all trace of 50 soldiers after an attack by Al-Qaeda elements enabled them to recapture control of the Al-Wahda stadium" outside Zinjibar, the commander serving with the 25th Mechanised Brigade told AFP on condition of anonymity.
He was unable to specify whether the troops had been killed, captured or deserted in the battle for the stadium which the army had recaptured from the militants only Friday.
The commander accused the defence ministry of abandoning the brigade's soldiers to their fate in the face of repeated attacks by the militants of the Partisans of Sharia (Islamic Law) movement who seized much of Zinjibar in late May.
"Senior ministry officials have stood idly while all this has been going on. But we are not going to surrender to the Al-Qaeda militants, we are going to fight to the last cartridge case," he said.
The Sanaa government says the militants in Zinjibar are allied with Al-Qaeda but the opposition accuses it of playing up a jihadist threat in a desperate attempt to keep embattled President Ali Abdullah Saleh in power.
Saleh had been a key US ally in its "war on terror" but has faced mass protests against his rule since January and is currently receiving treatment in neighbouring Saudi Arabia for blast wounds sustained in a bomb attack on his palace.
The ancestral homeland of slain jihadist leader Osama bin Laden, Yemen is the home of Al-Qaeda in the Arabian Peninsula, or AQAP, an affiliate of the global network accused of anti-US plots, including an attempt to blow up a US-bound aircraft on Christmas Day 2009.
Near the main southern city of Aden, troops opened fire on a vehicle they considered suspect Saturday, killing a civilian police identified as Nafee Bakchi and wounding four.