The S&P BSE Sensex ended down 157 points at 28,052 and the Nifty50 slipped 28 points to settle at 8,639.
Most chief ministers are in favour of the new tax regime.
Implementation of GST is expected to increase the gross domestic product of the country.
The government is banking on help from regional parties and rejigged numbers in the Rajya Sabha.
The S&P BSE Sensex ended up 134 points at 27,279 and the Nifty50 ended up 42 points at 8,371.
The Sensex fell 354 points or 1.3% to close at 27,512 levels.
The passing of the GST bill and the failure of India to acquire NSG membership is set to rule the agenda in Parliament.
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Government will make a fresh bid to pass crucial bills on GST and real estate in the last week of the Winter session.
PM Modi said his government has nothing to hide and would take everybody into confidence while dealing with it.
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'Modi had not discussed demonetization with me prior to his announcement on 8 November 2016. 'I learnt of it along with the rest of the country. 'I was not surprised when he did not discuss the issue with me prior to making the public announcement. 'It fitted in with his style of making dramatic announcements.' A fascinating excerpt from Pranab Mukherjee's The Presidential Years: 2012-2017.
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The S&P BSE Sensex slipped 305 points to end at 25,400 and the Nifty50 dropped 87 points at 7,783.
The government is keen to get the GST Bill approved during the Monsoon Session of Parliament ending on August 12.
Industry experts said the major pain point would be tax collection at source, which would create a rift between sellers and e-commerce companies.
Broader market outperformed with the S&P BSE Midcap index adding 0.7%, while S&P BSE Smallcap index gained 0.6%.
The Planning Commission was better than the Niti Aayog as it used to take up the issues of the states with the ministries concerned.
What Rajya Sabha can do for the states, no other House can do, the Prime Minister said.
GST rates would depend upon whether the commodity is used by a rich person or a common man
Criticising various provisions in the proposed GST regime, Moily said it will be a "technological nightmare" and the anti-profiteering provisions in it are "far too draconian."
The S&P BSE Sensex dipped 90 points to end at 27,747, after hitting an intra-day high of 28,014.
Analysts believe the GST could boost India's economic growth by up to 2 percentage points
German Chancellor Angela Merkel is on a three-day visit to India.
ICICI Bank was the top loser along with index heavyweights RIL, ITC and HDFC.
BSE Midcap and BSE Smallcap outperformed the frontline indices to gain 0.2% and 0.3%
The government on Tuesday said it may reconvene Parliament's Monsoon Session to get key legislations, including the pending GST bill, passed, maintaining it has an "open mind" on amendments to reform measures even as it began consultations with leaders of opposition parties.
Asian markets were trading mixed with shares in China witnessing profit taking after sharp gains in the previous session.
Jaitley said Modi government has put decisiveness and transparency on forefront in face of obstructionism.
The government on Wednesday decided not to hold special session of Parliament to pass the constitution amendment bill for rolling out Goods and Services Tax and will recommend to the President to prorogue the Monsoon Session.
Oppn MP says govt suffering from Cinderella syndrome, while CPI(M) alleges NDA sabotaging Bill
Participants will keenly watch fate of GST Bill in Parliament.
Gains in auto shares helped offset losses in select index heavyweights led by Infosys.
The rupee had gained 28 paise against the American currency to settle at nearly two-month high at 66.74 in Monday's trade.
According to DBS, GST has growth, inflation and fiscal implications.
The prime minister, who spoke in the Upper House as it bid farewell to 53 retiring MPs, noted that Rajya Sabha members are representatives of the states and the interest of their state should be a priority for them.
With just eight days left for the winter session, Jaitley and Parliamentary Affairs Minster M Venkaiah Naidu held consultations with Leader of Opposition in Rajya Sabha Ghulam Nabi Azad and Deputy Leader Anand Sharma.
Parliament on Thursday cleared the decks for the rollout of the historic Goods and Services Tax from July 1 as it approved four supporting legislations to usher in the one-nation-one-tax regime.
Aiyar has contended that this results in revenue loss, malpractices and even death of people consuming illicit liquor
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