US Defence Secretary Leon Panetta arrived in Djibouti on Tuesday for an hours-long visit during which he was to meet with President Ismael Omar Guelleh for talks on counter-terrorism measures.

"We'll be looking at what has developped into a very important partnership in dealing with counter-terrorism, with counter-piracy and with dealing with outreach into Africa," Panetta said shortly before arriving in this small Horn of Africa nation, home to Washington's only military base in Africa.

"You all know the significant efforts that have been made against Al-Qaeda in the FATA," he said, referring to a semi-autonomous tribal region in the northwest of Pakistan.

Now the challenges had "moved to key nodes, like Yemen and Somalia, and the efforts to go after them require important partnerships in that part of the world and Djibouti helps provide that partnership for operations that continue, not only against Al-Qaeda but Al Shebab as well".

Panetta arrived at US Camp Lemonier base early Tuesday, where more than 3,000 troops are stationed.

"Without getting into operational details, it's pretty clear that since (US-Yemeni cleric and terror suspect Anwar al-)Awlaki was taken down, that has impacted on AQAP (Al-Qaeda in the Arabian peninsula) and their capability but just like taking Ben Laden in Pakistan, the fact is AQAP, Al Qaeda still remain dangerous," he added.

"We have to continue operations to go after" them, he said.

A senior defence official said in his talks with the Djibouti leader Panetta would "probably" be discussing Djibouti's pending deployment of troops to the African Union mission in Somalia.

"The situation there is quite dynamic," he said.

A 9,700-strong African Union force comprising Burundian and Ugandan troops has so far failed to stamp out the Shebab rebels, who have been fighting to topple the Somali government for five years.