Fighting took place in the Sanaag region on the frontier between Puntland and Somaliland, and is reported to have lasted around four hours.
"We have attacked their bases and took control of their barracks. Our forces are now in full control of the Galgala Mountains and the enemy fled the area suffering heavy losses," Puntland Security Minister Yusuf Ahmed Qeyr told reporters.
Several members of the militia were killed and others taken prisoner, Qeyr said, without giving details of casualties on the security forces' side.
The offensive follows a similar attack on Mohamed Said Atom's militia on 26 July.
The warlord has been singled out by the UN Security Council for violating an arms embargo, and is believed to be a key supplier of arms to the Shebab group that controls large parts of southern and central Somalia.