Aquino, 61, served as the country’s 15th president from 2010 to 2016, and was succeeded in office by the incumbent, Rodrigo Duterte.
According to ABS-CBN News, he was hospitalised earlier on Thursday.
But he had been undergoing dialysis for at least five months and had recently undergone a heart operation, according to news reports.
Al Jazeera’s Jamela Alindogan, who is reporting from Manila, said sources have confirmed Aquino’s death.
“It is with profound sadness that I learned this morning of the passing of former President Benigno S. Aquino III,” Supreme Court Justice Marvic Leonen, who was appointed by Aquino in 2012, said in a statement.
“I knew him to be a kind man, driven by his passion to serve our people. I saw him carry his title with dignity and integrity,” added Leonen, who had also served as Aquino’s peace negotiator with the Moro Islamic Liberation Front.
In a statement, the European Union office in Manila said, “We mourn a friend who pushed for deepening of our relations.”
The German Embassy in Manila also issued a separate statement hailing Aquino for his role in “intensifying” ties between the Philippines and Germany during his term.
Chargé d’Affaires John Law of the US Embassy in Manila also extended his condolences to the family of Aquino, adding that his government “will always be thankful for our partnership” with the Philippines.
It was during Aquino’s administration that Manila took on China and filed a case before the Court of Arbitration at The Hague over maritime dispute in the South China Sea.
The Philippines won that landmark case a month after Aquino left office in 2016.
His six-year term saw a steady economic growth for the country.
But he had also faced controversy, including allegations of mismanagement in the aftermath of the 2013 Typhoon Haiyan, which left more than 6,000 people dead.
While known as being personally incorruptible, his name was tainted after critics and the opposition questioned the release of reallocated public funds to his allies in Congress.
He also approved a controversial government operation that left 44 commandos dead while pursuing a wanted Malaysian armed leader in the southern island of Mindanao.
That incident derailed the peace agreement with Muslim rebels that Aquino spearheaded during his time in office.
Aquino, also known in the Philippines by nickname Noynoy, was the only son of two of the country’s icons of democracy.
His mother, was the late former President Corazon Aquino, who was swept into power following the ouster of the dictator Ferdinand Marcos in 1986. During a failed military coup in 1989, he survived an assassination attempt by rogue soldiers while trying to defend his mother.
Aquino’s father and namesake, former senator Benigno Aquino Jr, was killed at the Manila international airport upon his return from exile in 1983. The assassination was seen as an impetus for the popular revolt and Marcos’ ouster three years later.
Before being elected as president in 2010, Aquino served as senator from 2007 to 2010, and as member of Congress from the province of Tarlac from 1998 to 2007.
The death of his mother in late 2009 led to an outpouring of support that catapulted Aquino into the presidency in the 2010 elections.
After leaving office in 2016, Aquino kept a low profile as allies of Duterte continued his criticism of him, and as he faced legal charges linked to the 2015 killing of the commandos. He was also the target of online attacks by supporters of the incumbent president.