It reported 407 new coronavirus cases within a 24-hour period, bringing the overall infections to 5,923. The Philippines had a total of 5,878 infections on the same day.
Indonesia also reported 24 more deaths, taking the whole death toll to 520, also the highest in the region. The number of recovered patients, meanwhile, was up by 59 to 607.
Dr Achmad Yurianto, the government spokesman on Covid-19 management, said that the latest data indicates ongoing transmission and called for Indonesians to take part in solving the "shared problem" together.
"We must make sure that we don't get infected while also we don't infect (others)," he said in a daily briefing.
Indonesia declared the Covid-19 a national disaster on Monday as the disease hit all 34 provinces across the vast archipelago, and opened its doors to international cooperation and humanitarian aids.
Following the declaration, President Joko Widodo called for greater transparency in the way his administration tackles the pandemic.
All information pertaining to the disease is now integrated in a single system under the national Covid-19 task force, and includes data about suspected cases, people under surveillance - whether they have displayed symptoms and are self-isolating - patients being treated, deaths and recovered patients.
As of Friday, there were 12,610 Covid-19 suspected infections across 34 provinces nationwide, aside from 173,732 people under surveillance.
The country has seen a jump in cases since last week as it is widening testing, addressing concerns over cases going undetected and insufficient testing proportionate to its huge population of nearly 270 million inhabitants.
The authorities have targeted carrying out about 10,000 tests a day in the near future, as it is procuring more PCR test machines.
Indonesia has so far administered more than 42,000 tests for the coronavirus, Dr Achmad said.
Professor Wiku Adisasmito, who leads the expert team in Indonesia's Covid-19 task force, said the outbreak may peak at around 100,000 infections and over 1,000 deaths in May.
Agreeing that the outbreak could peak in late May or early June, Dr Pandu Riono, an epidemiologist at University of Indonesia, predicted much higher infections and death toll.
He said that the current intervention in the form of large-scale social distancing, which he categorised as between mild and moderate, may result in between 1.25 million and 1.75 million infections, while deaths may range from 47,984 to 144,266. - The Straits Times/Asian News Network