The fighters are said to be "hiding in fewer than 10 houses" in the seafront district of Al-Giza al-Bahriya.
The pro-unity government force announced its full control of Sirte on Monday, after the last IS-controlled area fell to the UN-backed fighters.
However, a spokesman has told the BBC they are not declaring victory yet.
The operation's Ahmed Hadia told the BBC: "They've now taken control of the last area, but that does not mean military operations have ended."
