About 850 officers and men are in the battalion, which has been preparing for deployment since August.
"Nigeria had first promised to send troops to Somalia one-and-a-half years ago," Mohammed Adow, Al Jazeera's correspondent in Nairobi, the capital of nieghbouring Kenya, said.
Filling the AU contingent for Somalia up to its intended level of 8,000 troops has been beset by difficulty, Adow said, with only just over half that number now pledged to the force.
"Given the difficulties that there have been in getting countries to volunteer to Somalia - especailly with all the problems in Democratic Republic of Congo and Sudan's Darfur region - it is very difficult to get more troops for Somalia," he said.
Somalia's weak transitional government is facing a fresh surge in attacks from opposition fighters, threatening the fall of the capital Mogadishu.
Fighters from al-Shabab, a group which split from the armed Union of Islamic Courts (UIC), have control of several town and cities across Somalia.
The opposition controls the south of Somalia and has launched a series of raids on Ethiopian forces which have tried to defend the government, as well as 3,200 peacekeepers from Uganda and Burundi.
At least 10,000 civilians have been killed in two years of fighting, while a million people have been forced to flee their homes.
There has also been continued wrangling between Abdullahi Yusuf, Somalia's president, and Nur Hassan Hussein, who was sacked as prime minister by Yusuf last week.
The AU and Washington have backed Hussein and have so far refused to recognise
Mohamud Mohamed Guled, the new Somali prime minister, who Yusuf selected.
Ministers gathered at a meeting of the Inter Governmental Authority on Development (Igad), which has overseen the Somali peace process, agreed on Sunday to impose immediate sanctions on Guled.
|Yusuf's dismissal of the Somali prime minister has been criticised internationally [AFP]
"[Igad] regrets the attempts by president Abdullahi Yusuf to unconstitutionally appoint a new prime minister that Igad does not recognise and decides to impose sanctions on him and his associates immediately," it said in a statement, without elaborating.
Seyoum Mesfin, Ethiopia's foreign minister and chair of Igad's council of ministers, said that Yusuf could also face sanctions.
"If Yusuf is committed to continue on this path sanctions will be imposed on him too," he said.
The AU's peace and security council is due to hold talks in the Ethiopian capital on Monday to discuss Somalia.
The AU force to Somalia was originally intended to be filled by 8,000 soldiers but the bloc has since struggled to get commitments on troops from member countries.
Although Uganda and Burundi each have a battalion ready to go, they are seeking financial support and equipment so that they can be sent to Somalia.
Since it was founded in 2004, Somalia's transitional government has struggled to assert power across the Horn of Africa nation.
The country has been unstable since dictator Mohamed Siad Barre was overthrown in 1991.