Thousands of policemen and soldiers were deployed to ensure security.
"Let us become ecological stewards like how we protect the image of the Black Nazarene during the procession", said the priest.
Police say more than one million people have joined the Catholic ritual. Spain colonized the archipelago in the 16th century and spread the faith.
The Philippine Red Cross said it had assisted more than 600 devotees who were feeling unwell, or suffered injuries during the early stages of the parade as the crowd swelled and many clamoured to reach out towards the icon.
In 2016, two devotees were killed.
The near-suicidal displays of devotion have drawn frequent criticism in the Philippines, with some saying it resembles pagan worship.
The official also said that Estrada suspended work at the city hall except the department directly involved in the event.
"Filipino Catholicism follows the belief that the presence of a higher being can only be made real through the body and via the material", Maria Yohana Frias, an ethnology researcher at the National Museum of the Philippines, told AFP.
Hundreds of devotees join the first Black Nazarene procession in San Fernando, La Union Tuesday afternoon.
The city's top traffic cop, Superintendent Lucile Faycho, said the estimate was based on the number of attendees over the last six years.
The Black Nazarene is a life-sized, dark-colored, wooden sculpture of Jesus Christ that was brought to Manila by Augustinian friars in 1607.
"Filipinos who come to Quiapo... get a sense of being near the Lord, of the Lord touching them and of the Lord accompanying them... through hard challenges", Quiapo church parochial vicar Father Marvin Cruz told AFP.
"I came here because this is my devotion".
"We are 100 per cent ready", he said.