Dubey said he was opposing the bill not because of any religion, vedas or 'puranas' but because of the Supreme Court judgement.
The Supreme Court in December 2013 overturned a verdict of the Delhi High Court that had set aside Section 377 of the IPC asking the government to take a view on the controversial subject of decriminalising homosexuality.
The Delhi High Court in 2009 ruled that Section 377 was unconstitutional.
Tharoor, however, insisted on going ahead with the introduction of the Bill arguing that Dubey was quoting only "partially" from the Supreme Court judgement.
Tharoor was supported by BJD's Tathagata Satpathy.
However, in order to take the sense of the House, Deputy Speaker M Thambidurai put the motion to vote.
Tharoor pressed for division of votes in which the motion was negated by 71 'Noes' against 24 'yes'. There was one abstention.
Commenting on the development, Satpathy remarked "it is a very very sad day".
In a series of tweets later, Tharoor said he would make another attempt to introduce the bill.
"Intro of Pvt.Member's Bill 2 decriminalize consensual sex btwn consenting adults defeated in LS 71-24. Surprising to see such intolerance.
"Notice of intent to oppose introducn of Bill came so late there was no time 2 rally support. Will try again in future. We shall overcome!" he said.
Although the bill on decriminalising homosexuality was rejected at the introduction stage, Tharoor managed to introduce two other private member's bill pertaining to another amendment to the IPC and on Asylum seekers.
Over 70 other private members' bills pertaining to different issues were introduced in the Lok Sabha.
Among the private member's bills, Varun Gandhi (BJP) introduced a bill to provide for citizenship rules for refugees and asylum seekers.
Rajiv Satav (Cong) came up with a constitutional amendment bill to raise the age for contesting elections to Lok Sabha and state assemblies from 25 to 31 years.
At the same time, the bill sought to reduce the age for becoming Rajya Sabha members from 30 to 25 years.
Jagdambika Pal (BJP) introduced a bill for compulsory harvesting of rainwater in every residential, commercial establishment and government building.
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