The bill also seeks to declare the IIMs as institutes of national importance and abolish the post of visitor.
Currently, the President is the 'visitor' of the IIMs.
Moving the bill for consideration and passage, Mr. Javadekar said the aim of the bill is to remove the government's interference in IIMs.
He said the proposed legislation will usher in a new era of freedom in the IIMs and these institutes will not require to come to the government for various permissions and clearances.
"It is a historical bill which will bring a new era in management education in the country," he said, noting that financial transaction will be subject to CAG evaluation as the institutes run on tax payers' money.
He said it was not an ideal situation to run the IIMs from Delhi, noting the move is aimed at allowing autonomy to institutes which have created an eco-system for excellence in higher education.
The government will have only one representative in each BoG so that the institutes can take decisions independently, the minister said.
Participating in the debate on the bill, Congress leader Shashi Tharoor said it was a "remarkable moment when a minister surrenders (his) powers".
He said other ministers in the government should draw inspiration from Mr. Javadekar in doing so.
At the same time, the former minister criticised the government for not enhancing financial assistance to IITs and IIMs, saying they are reeling under funds crunch.
He suggested the government should have some say in determining fee structure in the IIMs as higher fees may badly hit students from the poor families.
He also pitched for clarity in having reservation in recruitment of faculty staff from SC and ST community.
Tharoor also slammed the government for removing the name of Rajiv Gandhi from the name of the Shillong IIM, saying it is "petty" of the government to stoop to such level.
Trinamool Congress leader Sougata Roy also praised the government for bringing the bill, saying it will further improve the functioning of the IIMs.
He said the fees in the IIMs were very high and urged the government to see that this does not deter the deserving students from admission.
M B Rajesh (CPI-M) also raised the issue of high fees in IIMs, saying the autonomous status should not lead to money- making by these institutions.
He sought to know from the government why it had appointed directors on the Boards of 10 IIMs on February 10, 2017, just a day after the IIM Bill was tabled in Parliament.
Pradhan sought to know from the government if it was aware of the fate of the students who pass out from the 5,500 private business schools and get paid a salary of as low as Rs 10,000 per month and are unable to repay the education loan.
Arvind Sawant (Shiv Sena) also appreciated Mr. Javadekar's move to grant the status of autonomous institution to the IIMs.
He sought the minister's attention towards private institutions demanding money from students at the time of admission.
B Ravindra Babu (TDP) too appreciated the HRD minister, saying the MPs in the House feel he is a "dynamic minister" and has been very liberal towards giving institutes of national importance to the bifurcated Andhra Pradesh.
BJP's Poonam Mahajan, praising the government, said effort must always be to ensure that the "wings of aspirations of the youth are not cut".
"Aspirations of the youth are country's hope. If the youth aspire, then only can we hope for a better tomorrow. It is a freedom movement for the IIMs. It is about freedom to think and pursue the goals by the youths," she said.
K Hari Babu (BJP) too praised Mr. Javadekar, saying everyone wants "power to be in their pocket" but the HRD minister has given up the position of being the chairperson on IIM Boards.
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(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)