The CIA agents arrived in the town of Bossaso on Wednesday and are holding meetings with Puntland's high-ranking officials, a Press TV correspondent reported.
This comes as US policy regarding Somalia has been hit with criticism. An international advocacy group blasted Washington in its recent report, saying US air strikes in the Horn of Africa country had caused devastation for aid workers on the ground.
"To stabilize the situation ... US policy requires a complete overhaul," reported Refugees International, adding that the US approach to terrorism is hypocritical and defines terror in a narrow manner.
The arrival of CIA officials in Puntland coincides with the entry of German secret agents in Somaliland, another breakaway Somali region.
Somaliland officials have confirmed the arrival of the German agents, adding that they had meetings with President Dahir Riyale Kahin.
It is not yet known why the secret agents have traveled to the Somali breakaway regions, which declared autonomy during the civil war; no country has so far recognized the regions.
Somalia has been without an effective central government since warlords toppled Mohamed Siad Barre in 1991. The ongoing violence in Somalia has resulted in the death and displacement of countless civilians.