The Philippines' interior and local government secretary Jonvic Remulla told a press conference in Manila there are "signs that point that the son is involved in the crime as well".
But he said Markle Jr, who alerted local police and the FBI to images he found in his father Thomas Markle Sr's belongings, was not yet being treated as a suspect.
More than 7000 photos and one video – all of under-age males and females of Asian, Latin and European descent, with some as young as 10 and 11 – were uncovered, Remulla said.
He described the images as "the most deplorable displays of impunity towards sexual activity that I have ever seen".
Markle Sr, who is estranged from Meghan, has been moved into a care home for dementia patients, prompting fears the FBI will not be able to interview him.
"We're determining if son is involved.There are signs that point that the son is involved in the crime as well but only as a person of interest so far," Remulla said:
"We will know in the next few days."
Markle Sr, who returned to the United States in May, has admitted paying for sex in the Philippines but denied possessing child abuse imagery.
Remulla said Markle Jr was still in Cebu City.
Meghan was "deeply distressed" by the allegations about her father and revealed she was sent a letter via the Metropolitan Police and Royalty and Specialist Protection seven years ago, which made "troubling and disturbing allegations" about Markle Sr, but that she was given assurances these were being investigated.
Thursday's development followed reports Markle Jr had also alerted the FBI to two storage units in Los Angeles, just days after a raid by Mexican police on a storage unit Markle Sr is said to have rented near his former home in Rosarito, Mexico.
A spokesman for Meghan declined to comment.
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