Niu and award-winning cinematographer Cao Yu were both charged with violating a law that bans Chinese nationals from entering Taiwanese military facilities, prosecutors said. The offence is punishable by a maximum five-year jail term.
"Niu was aware that Chinese nationals were barred from entering a military port but brought Cao there for scouting. However, they were not found to have pried in military secrets or committed forgery," said prosecutor Huang Yuan-kuang.
However, Cao got into the base in June last year by getting on a bus with the rest of Niu's crew members, who were on the approved list of visitors and also boarded a naval ship, according to prosecutors.
The navy decided to withdraw all assistance to Niu after the incident and reported him to prosecutors.
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"We thank everyone for their concerns on the case and we respect the judicial process for all follow-up matters," said the film's production company Atom Cinema.
"Filmmakers have often gone overboard and resorted to all possible means to make a great work and it's time to reflect," he wrote at the time.
Cao has twice won the cinematography gong at Taiwan's Golden Horse Film Awards, regarded as the Chinese-language Oscars.
"Military Paradise," set to hit theatres in the summer, is a comedy about a group of people on a frontline island preparing for a war that will probably never happen during the 1960s standoff between Taiwan and China, according to Atom Cinema.
However, security concerns linger despite eased political tensions as the former bitter rivals have been spying on each other since they split in 1949 after a civil war.
In 2011, Taiwan's defence ministry told travel agencies not to bring Chinese tourists to military camps, citing concerns that some might be spies, amid a security scare after one mainland group entered a base.