The man was allegedly using an "IMSI catcher", a device capable of mimicking a cell tower and snatching messages from the air in a one-to-three-kilometre (about 3,200-to-9,800-feet) radius.
Two Chinese men detained in February were accused of using the same device while driving near sensitive government and military locations in Manila.
National Bureau of Investigation spokesman Ferdinand Lavin told AFP the latest arrest was made Tuesday near the offices of the Philippine Commission on Elections (Comelec) after agents confirmed the IMSI was in operation.
"When we made the arrest, that was the third time he had come to Comelec," Lavin said, adding other locations visited included the Philippine Supreme Court, Department of Justice and US Embassy.
The arrested man held a passport issued by Macau, Lavin said, while a hired Filipino driver who cooperated with the operation was not detained. Macau is ruled by China.
Beijing on Wednesday said it was currently in communications with Manila to learn more about the situation while denying any attempt to tamper with Philippine elections.
"We will not and have no interest in interfering in such internal affairs of the Philippines," foreign ministry spokesman Guo Jiakun said when asked about the arrest at a daily press conference.
"We also advise individual politicians in the Philippines not to take the chance to hype up issues related to China, make something out of nothing and seize the opportunity to profit," Guo added.
Earlier this month, Beijing made its own allegations of spying, saying it had "destroyed" an intelligence network set up by a Philippine espionage agency and arrested three Filipino spies.
The Philippines' National Security Council (NSC) later said supposed confessions televised on Chinese state media appeared to have been "scripted, strongly suggesting that they were not made freely" and that a spy agency mentioned did not exist.
The espionage accusations come as the two countries confront each other over disputed territory in the South China Sea and as tensions rise over the Philippines' security ties with ally the United States.
Last week, NSC Assistant Director General Jonathan Malaya told a Senate hearing that his agency believed Beijing was likely behind online attacks aimed at influencing the coming mid-term polls.
The Chinese Embassy strongly denied the allegation.
The Philippines' May 12 elections will decide hundreds of seats in the House of Representatives and Senate as well as thousands of local positions.
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