Philippine Finance Secretary Cesar V Purisima said that the president has visited the mosque to check on its status.
The US$48-million mosque, the completion of which is now two months behind schedule, is partly funded by the monarch.
"The president (Aquino) visited it about a month ago. He met with the Sultan about it and he wanted to make sure that he checked the progress," said Purisima, who was in the country for His Majesty's 65th birthday celebration.
He said that Aquino "took a chopper and flew over it."
"I think they're finishing it," he added.
It was unclear, however, when the grand mosque would finally be completed, after contractor New Kanlaon Construction Inc missed its initial completion target last May 8.
Accommodating 800 male and 400 female worshippers, the mosque will also serve as a community centre for Muslim Mindanao.
It will house a library, a physical centre for the Darul Ifta (House of Opinion) and buildings for an Islamic tertiary institution.
Construction of the mosque began in 2009, when the Sultan made a three-day state visit to the Philippines.
Once completed, the mosque will be among the grandest in the country. It stands on a 5,000-square metre compound in Cotabato City.
The edifice, painted in white and gold, is as high as a 15-storey building with crescent moons adorning the golden domes. The minarets will be 43 metres high with pilot lights on top to avoid aerial accidents at night.