ridiculous to compare the home secretary of India to a terrorist," Krishna said during Question Hour in the Rajya Sabha.
On the eve of foreign ministers' talks between the two countries last month, Pillai had said that Pakistani spy agency Inter-Services Intelligence (ISI) played a "very significant role" in the 26/11 Mumbai terror attack.
Qureshi, during the joint press conference by the two foreign ministers in Pakistan, said the remarks by Pillai were "uncalled for" and made an apparent comparison between the home secretary's statement and the hate speeches by Lashkar-e-Taiba (LeT) founder Hafiz Saeed.
At that point, Krishna remained silent. But later in Delhi, he said there could be no comparison between the two statements.
"Such a comparison being made by a responsible foreign minister of a friendly country like Pakistan, I did not want to get in a slanging match there," Krishna said in response to a question by BJP member and Deputy Leader of Opposition in the house SS Ahluwalia.
The minister defended Pillai's statement, saying it was only a reflection of the information revealed in interrogations of Mumbai terror attack mastermind David Coleman Headley.
After repeatedly being urged by the BJP members to give a reason for remaining quite when Pakistan's foreign minister made the statement and later talking about the ill-timing of Pillai's comment, Krishna said a reply there would have been of no use.
"It was of no use to respond to him (Qureshi) there," he said.
The minister, however, maintained that the comment made by Pillai was wrongly timed. "Home Secretary is a distinguished civil servant... still I maintain the timing of the statement was wrong," Krishna said.
Answering a question on whether issues like Kashmir, Siachen and Sir Creek were taken up with Pakistan, Krishna said the government wants to take a step by step approach.
"We wanted a graduate, step by step approach in solving our problems. But we had our position clear. India is ready to discuss everything," he said.
"We have nothing to be afraid of. Our conscience is clear. Whatever decisions we have taken on these issues have been taken with full responsibility," he said.
Krishna added that the attention of the Pakistan government has been drawn to the repeated efforts by the jihadist forces in disrupting peace in India. "It doesn't help in reducing trust deficit," he said.
Expressing India's willingness to carry forward the composite dialogue, the minister said Pakistan's response to India's gesture is what matters.
"We want to settle all our differences with that country. Pakistan will decide their response to the broad gesture by India," Krishna said.
The minister, however, added that a host of issues had 'broad consensus' between the two nations, which included freeing of fishermen, people to people contact and trade and commerce.