Also cancelled are several exchanges focusing on humanitarian and disaster relief issues, and meetings on the stopping the spread of weapons of mass destruction.
However, the six-nation talks on North Korea's nuclear programme will not be affected.
Commenting on the Chinese decision, Upton said the Pentagon regretted the "missed opportunities" which he said were caused by "China's continued politicisation of our military relationship."
Washington is Taiwan's most important ally and the island relies on US arms to maintain the military balance against Chinese positions on the opposite side of the Taiwan Strait.
|US is planning to sell $6.5bn worth of weapons to Taiwan's military [AP]
On Friday US defence officials notified congress of a proposed sale of $6.5bn worth of advanced weapons to Taiwan.
The plan includes the sale of advanced Patriot missile defences, Apache attack helicopters, and submarine launched anti-ship missiles.
The announcement met with an angry reaction from Beijing, with Chinese officials warning that the proposed sale would undermine China-US ties.
Speaking on Saturday Liu Jianchao, spokesman for the Chinese foreign ministry, said the weapons sale was an interference in China's internal affairs, endangered national security and would upset the peaceful development of cross-strait relations.
"It is only natural that this move would stir up strong indignation of the Chinese government and people," Liu said, according to Xinhua, the Chinese state news agency.
"We sternly warn the United States that there is only one China in the world, and that Taiwan is a part of China."
US diplomats in Beijing were also summoned to hear a strong formal protest at the proposed sale.
China has a long history of opposition to US arms sales to Taiwan, which it regards as a renegade province.
Taiwan split from mainland China in 1949 when nationalist Kuomintang forces retreated to the island at the end of civil war that brought Mao Zedong's communists to power.
Since then Beijing has vowed to eventually reunify Taiwan with the mainland, by force if necessary.
As such it regards any outside involvement in the issue as interference in its domestic affairs.
The United States broke off formal relations with Taiwan when it switched diplomatic recognition to Beijing in the 1970s.
But under the terms of the US Taiwan Relations Act Washington says it reserves the right to sell the island sufficient weaponry to maintain its self-defence.