China had objected earlier to my visit to Tawang when I was the foreign minister," Mukherjee told reporters on the sidelines of an India-Bangladesh dialogue in New Delhi.
Earlier in the day, external affairs ministry spokesman Vishnu Prakash said: "We express our disappointment and concern over the statement made by the Chinese ministry of foreign affairs since this does not help the process of ongoing negotiations on the boundary question."
He said Arunachal Pradesh, which borders Tibet, was an "integral and inalienable part of India" and its people are "proud participants in the mainstream of India's vibrant democracy".
He said China was "well aware of this position" of the Indian government.
External Affairs Minister S M Krishna added: "I have said it in parliament that Arunachal Pradesh is an integral part of India. We rest it at that."
Their comments followed a Chinese foreign ministry statement that Beijing "is strongly dissatisfied with the visit to the disputed region by the Indian leader disregarding China's serious concerns".
"We demand the Indian side address China's serious concerns and not trigger disturbance in the disputed region so as to facilitate the healthy development of China-India relations," spokesman Ma Zhaoxu said in Beijing.
Ma said China and India had never officially settled the demarcation of their border, and China's stance on the eastern section of the China-India border was consistent and clear-cut.
Beijing in 2003 gave up its territorial claim over India's Sikkim state but maintains that nearly all of Arunachal Pradesh belongs to it. The mountainous state of Arunachal shares a 1,030 km unfenced border with China.
Also Tuesday, China's ambassador to India, Zhang Yan, called on the Indian foreign ministry to convey his government's stand on the prime minister's visit to Arunachal Pradesh.
The Chinese statement, however, made no reference by name to Manmohan Singh, who visited Arunachal Pradesh October 3 to campaign for the Congress in assembly elections that took place in the state Tuesday.
At the same time, Prakash said that India was "committed to resolving outstanding differences with China in a fair, reasonable and mutually acceptable manner, while ensuring that such differences are not allowed to affect the positive development of bilateral relations".
"We hope that the Chinese side will similarly abide by this understanding."
An Indian lawmaker also slammed Beijing for criticizing Manmohan Singh's visit to Arunachal Pradesh.
"It is simply blasphemous on the part of China to oppose or express dissatisfaction over the visit of our prime minister to Arunachal Pradesh," Takam Sanjay, a ruling Congress MP in the Lok Sabha from Arunachal Pradesh said.