Ethnic division, political tension, economic decay and international isolation are just part of the legacy he has inherited from his predecessor, General Sani Abacha, who died, an official statement recorded, of a heart attack last Monday.
Political prisoners and plans to restore constitutional government will be pressing issues at the top of his agenda. On the streets, there has been jubilation in some quarters at the passing of Nigeria's most uncompromising head of state, and unease in others over what the future under General Abubakar might hold.
"Again, the government of our country appears to be an exclusively military matter," one merchant banker in the commercial capital, Lagos, said yesterday. "We are still looking for any sign that this change will empower the people."
Popular considerations have rarely weighed heavily on the minds of the military men who have ruled the country since the collapse of the civilian Second Republic amidst allegations of fraud, corruption and mismanagement in 1983.
General Abubakar's priority will be to try to overcome an apparent split within the military over what role it should play in the political process, which could fatally weaken his position.
General Abacha's closest supporters advocated following a path well-trodden by other military rulers in west Africa, such as Jerry Rawlings in Ghana, or Blaise Compaore in Burkina Faso, who have successfully transformed themselves into constitutional, civilian presidents.
Others, including Nigeria's chief of army staff, Major-General Ishaya Bamaiyi, have publicly called for the military to distance itself from politics. This call for a full return to the barracks, they argue, is a vital precondition for a genuine, stable democracy. Privately, they fear that further engagement in politics, particularly in the manner proposed by General Abacha, might prove so corrosive as to fatally undermine the integrity of the military as an effective institution.
General Abubakar has never publicly aligned himself with either tendency, although his reputation as a professional soldier - he served with the United Nations in Lebanon in the Eighties - is unlikely to endear him to those looking to cement the military's role in politics, such as Lieutenant- General Jerry Useni, minister of the Federal Capital Territory (FCT).
"He's unlikely to have everyone's confidence," remarked a Western diplomat in the capital, Abuja, "and his position remains far from secure."
If he is to please Washington and Europe, Nigeria's new head of state will need to release high-profile detainees, such as the former presidential aspirant, Chief Moshood Abiola, who was charged with treason in 1994 after declaring himself the winner of elections annulled by the military a year earlier. Friday marks the fifth anniversary of that annulment, and could provide the opportunity for hitherto divided and demoralised radical opposition groups, operating principally in Chief Abiola's Yoruba south-west, to put on a show of strength.
Also in prison is the former head of state and respected international statesman, General Olusegun Obasanjo. Such a move would antagonise Abacha loyalists, however, and might provoke hostility elsewhere in the northern, Islamic, establishment which has traditionally dominated Nigerian politics.
General Abubakar, although a Muslim, is from a minority tribe in the north and will find it difficult to rule without the support of the Hausa- Fulani majority.
The most awkward problem with which the new leadership will have to deal is what to do with General Abacha's programme to restore civilian rule, due to be completed by October.
A government spokesman, Air Vice Marshal Isaac Alfa said in Abuja that the regime would stick to the timetable to restore civilian rule by 1 October, as Abacha promised. However, he did not say whether the August date for presidential elections would be respected.
The democracy process under General Abacha had been widely criticised abroad and generated little enthusiasm in Nigeria. The five registered political parties lacked any ideology, appearing only as vehicles for the individual ambition of wealthy personalities. All had eagerly pressed for the adoption of General Abacha as their consensus candidate, leading radical groups to call for the scrapping of the entire process.
The new head of state, in any case, may find it technically impossible to proceed with a process which appeared to have as its only purpose the installment of General Abacha as constitutional president.
However, a return to the free-for-all of open political competition also carries risks, with the civilian political class prone to influence-peddling and money politics.
In addition, General Abu-bakar inherits an economy in a state of collapse. Health care, education and social infrastructure are in a woeful condition. Even petrol is in short supply - in a country which produces more than two million barrels of oil a day.
As with Nigeria's political problems, economic distress, while not created by General Abacha, worsened under his tenure. According to recent World Bank figures, Nigeria now ranks amongst the 20 poorest countries in the world, despite 20 years as one of the world's biggest oil producers.
General Abubakar has declared a week of national mourning, in which the politicking now likely to take place will happen in private. To the nation, the new head of state has appealed only for "all hands on deck".
"We're hoping it is an appeal for unity to turn the country around" said one diplomat, "not a preparation to get into the lifeboats".
Antony Goldman is senior Africa editor at the Economist Intelligence UnitReuse content