The border agents "have discovered five unidentified bodies of irregular migrants of African origin during a patrol in the Dahr al-Khass area" near the Tunisian boundary, the interior ministry said in a statement.
Since mid-July, Libyan border guards have rescued dozens of migrants who said Tunisian authorities had taken them to an uninhabited area near Al-Assah, 150 kilometres (93 miles) west of Tripoli and around 15 kilometres inside Libyan territory.
AFP correspondents have seen groups of migrants visibly exhausted and dehydrated after trekking through the desert in the scorching summer heat.
Online videos published by border agents show migrants arriving by foot across the Tunisian border.
In early July, hundreds of migrants from sub-Saharan African countries were driven out of the Tunisian port city of Sfax as racial tensions flared following the death of a Tunisian man in a clash between locals and migrants.
About 130 kilometres from the Italian island of Lampedusa, Tunisia is a gateway for migrants and asylum-seekers attempting dangerous sea voyages in hopes of a better life in Europe.
On July 18, independent UN experts urged Tunisia to stop the "collective expulsions" of migrants, following reports that dozens had been left by Tunisian police in the desert near Libya.
"We call on the authorities to immediately halt any further deportations and to continue and expand humanitarian access to a dangerous area on the Tunisian-Libyan border where many, including pregnant women and children, have already been deported," the expert panel said in a statement.
In Libya, human traffickers have long profited from the chaos since the 2011 overthrow of dictator Moamer Kadhafi, and the country has faced accusations of migrant abuse.
Rights groups have alleged horrific treatment of migrants at the hands of smuggling gangs and inside state-run detention centres. Authorities and armed groups operating under state auspices have repeatedly been accused of torture, rape and other abuses.
The country hosts an estimated 600,000 sub-Saharan African migrants.
