National police chief Khalid Abu Bakar revealed the findings at a press conference a day after the government announced on Sunday the discovery of camps and graves, the first such sites found in Malaysia since a regional human-trafficking crisis erupted earlier this month.
"[Authorities] found 139 suspected graves. They are not sure how many bodies are inside each grave," General Khalid said.
He added that the number and size of the 28 camps found suggested they might have housed a combined hundreds of people.
The largest could hold up to 300 people, another had a capacity of 100, while the rest could hold about 20 each, he said.
The first decomposed body was brought down to a police camp set up at the foot of the mountains where the graves were discovered on Monday evening.
The operation took nearly five hours due to the rough terrain.
"The body was only bones and little bit of clothing on it," Padang Besar police officer-in-charge Rizani Che Ismail said.
He said the cause of death was not immediately apparent.
The discovery was the latest evidence of the lethal nature of the region's human-trafficking trade and has been condemned by Malaysia's prime minister Najib Razak.
"I am deeply concerned with graves found on Malaysian soil purportedly connected to people smuggling," Mr Najib said on his Facebook page.
"We will find those responsible."
However, a politician from the Malaysian opposition has accused authorities of colluding with human traffickers.
"Large numbers, you're talking people in the hundreds are being brought across the border," Rasiah Sivarasa said.
"Extensive ransoms are being collected from their families back in Bangladesh or wherever they come from.
"Some of them who can't pay these ransoms are sold as slaves to plantations, to fishing boats.
"I cannot believe, therefore, that the authorities do not know about this."
Thai prime minister offers medical aid to migrants at sea
Police in neighbouring Thailand in early May found secret human-trafficking camps on their side of the border and dozens of shallow graves.
Malaysian officials had subsequently dismissed the suggestion that similar sites existed on Malaysian soil.
General Khalid said the camps and graves were in mountainous jungle areas that were difficult to reach.
He declined to respond to a later question on how such an extensive system of camps could have existed without detection by authorities and whether the complicity of corrupt officials was suspected.
Rights groups have long accused Malaysian authorities of not doing enough to contain people smuggling.
General Khalid said authorities were in the painstaking process of exhuming and conducting post-mortem exams on the remains.
Thailand launched a crackdown on people smuggling following the discovery of its mass graves and is not allowing migrant boats to land.
However, prime minister Prayuth Chan-ocha on Monday said the Thai navy would help those in medical need.
"I have ordered the navy to take our boats and set up a floating command centre to help those who are hurt," he said.
The move appears to have caused nervous traffickers to abandon their human cargo at sea, leaving boats filled with hundreds of starving migrants seeking to land in Malaysia, Thailand and Indonesia.
After initially turning them away, Malaysia and Indonesia last week bowed to international pressure, saying they would admit boat people pending their repatriation or resettlement elsewhere.