They were both shot on Friday during the final day of the island's election campaign, but their conditions were not life-threatening, an aide said.
President Chen Shui-bian was hit in the stomach and Vice President Annette Lu was hit in the knee as they were driven through the streets of the southern town of Tainan in campaigning for Saturday's presidential vote, said Chen's spokesman Chiou I-jen.
They were rushed to the Chi Mei hospital in the town 300 kilometres south of Taipei but their lives were not in danger and the elections were scheduled to go ahead as planned, Chiou told reporters in Taipei.
Nobody has claimed responsibility for the shooting which comes at the end of a bitter and divisive campaign fought over the island's relations with mainland China. It was unclear how the incident would affect the poll.
"We confirm that at 1.45pm the president when campaigning in Tainan was shot," said Chiou, the secretary general of the presidential office, adding that doctors had removed a bullet from the president's stomach.
"They did not suffer life-threatening injuries. They urge the public to cool down."
Chiou I-jen, spokesman
"They did not suffer life-threatening injuries. They urge the public to cool down," Chiou said at a news conference. He added that "the president is conscious" and "can still direct the nation's affairs."
Elections to continue
The presidential ballot will go ahead as planned on Saturday, an election official said.
Television pictures showed Chen waving to the crowds from the back of a red four wheel-drive vehicle alongside Lu, with motorcycle outriders by his side.
A white-jacketed security guard was seen standing directly behind Lu as part of a large motorcade. The shooting incident was not shown by local television, but the red car was later shown being driven away with what appeared to be a bullet hole in the windscreen.
"The bullet hit ... Vice President Annette Lu before hitting Chen Shui-bian's stomach," said lawmaker Wang Sing-nan from the ruling Democratic Progressive Party, who was with Chen at the hospital.
"The vice president first felt pain in her knee and she thought it was caused by firecrackers," Chiou said. "Then the president felt some wetness on his stomach area, and then they realised something was wrong."
Last minute campaigning
Chen has been a vocal in his desire
of a referendum on sovereignty
Both Chen and opposition challenger Lien Chan spent Friday doing last-minute campaigning in the south of the island ahead of the election in which the two rivals are reported to be running neck and neck.
The National Security Council said it had stepped up security for opposition Kuomintang (KMT) candidate Chen and his deputy James Soong following the shooting. Both the Kuomintang and the DPP were due to hold final campaign rallies on Friday night.
The campaign has been long and spiteful, with much acrimony over Chen's plans to hold a referendum vote separate from the presidential election centred on relations between the island and mainland China.
The referendum is seen as an attempt by Chen to push the island further down the road towards independence, something China has threatened to oppose by military force.
China and Taiwan split at the end of a civil war in 1949. Despite over half a century of de facto independent rule on Taiwan, the government in Beijing still claims the island is a renegade province which must be brought back under its rule.