Yangon-based Unity journal quoted villagers as saying the sprawling factory in Pauk, a township in central Myanmar's Magway region, was for production of chemical weapons - a claim the government decried as "totally baseless."
According to roadside vendors, police have taken all Jan 25 editions of the journal off the shelves.
State-run television reported the arrests Wednesday night.
Myanmar only recently emerged from a half century of brutal military rule. Since a nominally civilian government was installed in 2011, it has implemented sweeping reforms, from releasing political prisoners to freeing up the press. But media watchdogs say that reporters still occasionally face intimidation and arrests, especially in rural areas, and that the climate appears to be worsening.
The journal's CEO, Tin San, told The Associated Press just before his own arrest Saturday that the publication's Pauk township reporter, Lu Maw Naing, had been hauled in the night before, apparently because of the article.
Three hours later, three other reporters were taken in, according to Tin San's nephew Aung Win Tun.
State-run television said the detained had violated the 1923 State Secrets Act by entering a prohibited area and disclosing state secrets.
Deputy information minister Ye Htut could not be reached for comment. He has acknowledged in local media that it was a Defence Ministry factory, but denied links to chemical weapons.
The claims are "totally baseless," he told Irrawaddy, a Thailand-based online news site.
"The journal only quotes local people," Ye Htut said, defending the arrests of journalists following allegations that the government was starting to trample on newfound press freedoms. "It is a national security issue, and even a country like the United States would respond the same way on these matters."