The government, however, blamed the opposition for not participating in the debate and said it was "tragic" that the Bill had to be passed in the din.
It asserted that the measure had to be passed for the "welfare of the poor and country" and cannot wait for those who are unable to "digest" the action against black money and corruption.
Congress leader Mallikarjun Kharge said, "We want that Income Tax Amendment Act should come through the rules. The amendments proposed by the Opposition MPs and leaders should also be kept in mind before taking the assent from the President."
"The government has been totally undemocratic, dictatorial, authoritarian in passing such an important bill without discussion amidst din. It has taken advantage of the superior numbers to avoid discussion. It is unfortunate that we did not get any relief from the Chair.
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"I had written to the Speaker (Lok Sabha) in the morning that this bill should not be allowed to be passed in the din. But what we apprehended happened. Inspite of all of our protest, this bill was passed. The very purpose of the bill was sort of defeated," said Saugata Roy TMC MP.
Amid fierce slogan shouting by the opposition, Finance Minister Arun Jaitley said the Taxation Laws (2nd Amendment) Bill, 2016 was brought after it came to the government's notice that some people were trying to illegally exchange the demonetised Rs 1000 and Rs 500 currency note.
Roy said that the government is "stubbornly" sticking to its stand that there will be no discussion but "we (opposition) are all together and we will continue to press for discussion" under a rule which entails voting.
"The way the government is treating Parliament and
willingly or unwillingly the Chair is allowing this to happen, this will be written in the history as the black day in Parliament," Salim said.
Union Minister Ravi Shankar Prasad dismissed the opposition's charge.
"It is written in the Constitution what is a money bill or not. Those bills which the Speaker certifies are considered money bill.
"As far as my knowledge about law is concerned, amendments in relation to Income Tax is a money bill. Where is the scope for discussion on this?" he asked.
"If somebody has problems with that than I will ask them to read Mahatma Gandhi, Deendayal Upadhyay, Ram Manohar Lohia, then you will know what we dream of," he said.
Minister of State Civil Aviation Jayant Sinha said that the unaccounted money that is coming into the bank will now be acknowledged in a legal way.
"It is off course tragic that it had to be passed in the din. The opposition is not able to digest the fact that these measures against black money and corruption are so wildly popular and have had an impact," he said adding that the government wanted discussions and "since the opposition did not want any discussion, they shouted".
Union Minister Harsh Vardhan said that it is "unfortunate" that the Opposition did not participate in it.
"It is a very important bill which has been formulated by the Prime Minister and and Finance Minister for the welfare of the poor. I believe this is a historic step where the black money is being utilized for welfare of poor and that too with their agreement.
"What else will be a bigger consensus for the country. If opposition had participated, it would have been better. If the government is working for the welfare of the poor and country, then it cannot wait," he said.
"The right of the members to move amendment is totally curtailed which is truly undemocratic, which is not heard in the history of parliamentary democratic system. If this is the system we are following, when the House is in big turmoil, we can pass any legislation.
"GST bill can be passed, even Constitutional Amendment bill can be passed. This is an insult to parliamentary democratic system and it is weakening it which is quite unfortunate. This can never be agreed upon.