Yesterday's announcement at the State Department stressed Lee Teng-hui would come to the United States "in a strictly private capacity and will not undertake any official activities".
The State Department spokesman Nicholas Burns said the decision does not represent a change in US policy, which is based on the view there is only one China.
Mr Burns said Peking was told about the announcement in advance. He would not comment on the Chinese reaction except to say: "I would describe it as a negative reaction.
"Americans treasure the rights of freedom of speech and freedom of travel and believe others should enjoy these privileges," he said.
Mr Lee has been invited to address the 8-11 June Alumni Reunion Weekend at Cornell's campus in Ithaca, New York. No president of Taiwan has been permitted to visit the country since the United States in 1979 recognised Peking as the sole government of China and downgraded to "unofficial" its relations to Taiwan.
Under this policy, the State Department has limited travel in the United States for Taiwan's top officials to transit to or from third countries. The Cornell campus is far from transit airports.
En route to Central America last year, Mr Lee paused in Honolulu without being allowed to stay overnight, prompting protests in Congress about discourtesy to an American-educated friend of democracy. Mr Lee was refused permission to enter the United States for the 1994 reunion.
Earlier this month, the House voted 396-0 and the Senate 97-1 for resolutions urging the White House to allow Mr Lee to go to Cornell.