The Taiwanese man who was arrested at the scene said he was expressing his political views and had stolen the sword from a nearby history museum, police told AFP.
The presidential office in the centre of the capital Taipei is the headquarters of Taiwan's Beijing-sceptic President Tsai Ing-wen.
Relations with Chinese authorities have deteriorated since she took office last year as she has refused to agree to Beijing's stance that Taiwan is part of "one China".
The island is a self-ruling democracy, but Beijing still sees it as part of its territory to be reunited.
"A Chinese national flag was found in his backpack. He said he wanted to express his political stance by going to the presidential office," the official said.
The man, identified only by his family name Lu, stabbed the officer as he tried to stop him entering the complex from a side gate, said presidential spokesman Alex Huang.
Lu is currently being questioned by police.
The injured guard is in a stable condition after being rushed to hospital for treatment, Huang said.
TV footage showed Lu being carried away by four officers and put inside a police car at a side entrance to the presidential office, which has been cordoned off since the attack.
The complex and its surroundings have been the target of attacks before.
In November 2014 a driver tried to smash his vehicle into the front door of the nearby presidential residence, saying he was protesting the health policies of Tsai's predecessor Ma Ying-jeou, who was in power at the time.
There were no injuries from either incident, apart from one of the drivers who was wounded.
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