The state-run Central News Agency quoted Timothy Yang, head of the Presidential Office, as saying security around the office block will be improved as soon as possible.
"I have asked that a security-enhancing special task force be immediately established at the Presidential Office," he said.
CNA reported Chang Teh-cheng, 41, rammed his truck into the part of the building where the cars carrying President Ma Ying-jeou, Vice President Wu Den-yih and other senior government officials park each day.
Police said he drove the truck through public railings and a bullet-proof security screen, and up a flight of stairs before jamming it into the gate leading to the office area's main building.
The driver was knocked unconscious and taken to the nearby National Taiwan University Hospital for serious, but not life-threatening, injuries, police said. No one else was injured.
Police said they will try to establish Chang's motive for the breach of security.
CNA reported it was the most serious security breach in years involving the presidential office.
Ma was not in the country at the time, having left Friday for the island republic of Sao Tome and Principe, lying in the Gulf of Guinea, off the western equatorial coast of central Africa.
CNA reported Ma is on the first leg of an eight-day three-nation tour. He goes to Burkina Faso on the African mainland before traveling to Honduras in Central America to attend the Jan. 27 inauguration of Honduran President-elect Juan Orlando Hernandez.
Ma is hoping to boost trade with Sao Tome, which established diplomatic relations with Taiwan 17 years ago.
The visit is the president's latest round of diplomatic tours designed to cement relations with countries that recognize Taiwan as independent from the People's Republic of China.
Ma and his entourage need to persuade countries to start or continue with business relations, even though they may not recognize Taiwan -- officially called Republic of China -- as independent.
Taiwan remains defiant against the claim by the ruling Communist Party in Beijing that Taiwan is a province of the PRC.
Beijing claims Taiwan has been an integral part of China since 1949 when the nationalist army retreated there following its defeat on the mainland at the hands of the the Communists.
Beijing generally is quick to condemn moves by Taipei to establish diplomatic relations with countries. It decries countries that maintain links or wish to establish them with Taipei.
But in a mood of realpolitik in November, Beijing reopened its diplomatic mission in Sao Tome -- potentially rich in offshore oil and natural gas deposits. Beijing cut off official diplomatic relations when Sao Tome recognized Taiwan.
Africa has been an important market for China's expansionist global business empires, especially in the field of oil and natural gas development in the past decade.
China-U.S. Focus, a non-government, non-profit organization based in Hong Kong, said in November at the time of Beijing's re-engagement with Sao Tome the move could help boost significantly the island nation's flagging economic prosperity.
Recent times have been hard for Sao Tome's less than 200,000 population because of poor cocoa harvests.
"There is every geological reason to assume that the territorial waters of both Sao Tome and Principe also hold exploitable reserves of oil and gas," China-U.S. Focus said.
"China intends to build a massive deep-water port in Sao Tome, which will make exporting oil easier and generally facilitate sea-borne commerce. Sao Tome and Principe has, for several years, been seeking outside assistance for such construction," China-U.S. Focus reported.