The President, popularly known as Jokowi, was not invited to the reunion event held by the 212 alumni in the area adjacent to the State Palace.
Jokowi, who is a former Jakarta governor, carried out activities in Bogor, one of which was the installment of the electricity project of the state power firm PLN.
PLN spokesman Agung Murdifi had earlier confirmed that the electricity installment would be attended by the President.
"Yes, he will be here soon, we are preparing for the President`s arrival," he said when contacted by telephone.
The President was slated to carry out a number of agendas in the city of Bogor as planned the day before.
While in Jakarta, masses from various parts of the Jabodetabek (Jakarta, Bogor, Depok, Tangerang and Bekasi) region and even outside Java have packed the Monas area since Saturday night.
They continued to arrive by using transportation modes including buses, private cars, even some of them using bicycles.
The participants carried flags with the words tawheed, Red and White flag, and some raised the Palestinian flag.
The organizers have estimated that some three million participants took part in the 212 alumni reunion rally.
"We estimate that three million are taking part in this morning 212 Alumni Reunion, or the same number as that last year," Novel Bamukmin, the event chief organizer, said.
Bamukmin explained that participants had been arriving since Saturday from a number of regions. The organizers, he said, had prepared command posts to accommodate them at a number of mosques around Monas.
He said the rally had no political purpose. It is basically a religious tourism and effort to uphold `tawheed` (faith in one God).
"There is no political element. We do not allow other flags to fly, besides Merah Putih and the Tawheed flag. We do not allow party flags," said Novel.
The 212 rally alumni was established to gather people who were involved in the rally on Dec 2, 2016 to call for the prosecution of then-Jakarta governor Basuki Tjahaja Purnama or Ahok for blasphemy.
Reporting by Hanni Sofia
Edigint by Sri Haryati