The announcement came two days after political and medical officials said that 78-year-old Mutharika had died following a heart attack.
The long official silence had raised fears of a power struggle between the ruling party and Vice President Joyce Banda, who was booted from its ranks in 2010 in a bitter succession battle with Mutharika.
After a series of Orwellian announcements by state media and the Information Minister Patricia Kaliati, who insisted late Friday that Mutharika was still alive, the government put out an official statement that the president had in fact died on Thursday.
“It is with the most profound grief, greatest sorrow, and reverential acceptance of God’s will, that the Office of the President and Cabinet announces to the Malawian nation the untimely passing of his excellency” Mutharika, said the statement sent to AFP.
Mutharika suffered a heart attack at State House at 11:15 am Thursday, and was pronounced dead upon arrival at a military hospital in South Africa the same day, said the statement signed by Bright Msaka, secretary to the president.
“The constitution of the Republic of Malawi shall be strictly adhered to in managing the transition,” said the statement, urging “all Malawians to remain united and peaceful during this period and at all times.”
Malawi declared 10 days of mourning from Saturday, with flags at half-staff. The statement did not say when Mutharika’s body would return from South Africa.
During the news blackout in Malawi, political insiders said that Mutharika’s Democratic Progressive Party was looking for ways to prevent Banda from taking office.
Banda spoke on radio Friday to urge the nation to follow the constitution, which calls for the vice president to take over.
But Kaliati, the information minister, later lashed out at Banda and claimed Mutharika was “still alive and there is no vacancy in government.”
She also insisted that Banda could not take the presidency because the vice president had “formed her own opposition party”.
Mutharika expelled Banda after he anointed his brother Peter as heir apparent, drawing accusations that he was trying to create a political dynasty and seal power with his office and his family.
Banda formed her own People’s Party and became a fierce critic of Mutharika, accusing him of running the economy into the ground.
Washington, which last year joined many donors in suspending aid to Malawi over concerns about Mutharika’s governance, has thrown its support behind Banda.
“Malawi’s constitution lays out a clear path for succession and we expect it to be observed,” Johnnie Carson, the US assistant secretary of state for African affairs, said in a statement.
Mutharika, a former World Bank economist who first came to power in 2004, was re-elected with a sweeping majority in 2009 as president of the poor southern African country.
But he increasingly came under fire for attempts to rein in the media and to shield the government from public criticism.
His feuds with donors and lenders such as the International Monetary Fund have hamstrung the economy in this aid-dependent nation. Now Malawi is suffering from shortages of foreign currency that have left it unable to import enough fuel.
When public frustration erupted into nationwide street protests in July, police shot 19 people dead. Last month, a broad coalition of rights groups called on Mutharika to resign.