Singh said nobody anticipated that Scindia would quit the party.
The Congress also said they would mention the matter before the Supreme Court on Monday.
The speaker had disqualified nine Congress MLAs under the anti-defection law hours after imposition of President's rule in the state on March 27, a day before the state government was scheduled to go for a floor test in the assembly.
Hours after President's rule was imposed in Uttarakhand, nine rebel Congress MLAs were disqualified from the state assembly.
The apex court directed that the proceedings of the floor test should be video-graphed. The President's rule, imposed on the state on March 27, was suspended for the proceedings of floor test.
With the Congress government in crisis in Uttarakhand after nine party members of Legislative Assembly, including a minister, joined hands with the opposition Bharatiya Janata Party overnight, Chief Minister Harish Rawat on Saturday asserted that the welfare of the state was his priority and added that he would tender his resignation if he was not able to prove majority.
The by-elections are being held to fill the vacancies caused by the disqualification of 17 rebel Congress and Janata Dal-Secular MLAs, whose rebellion led to the collapse of the H D Kumaraswamy-led coalition government in July and paved the way for the BJP to come to power.
The bench was also of the view that no interim order can be obtained unless the parties see the grounds for proclamation for President's rule.
Minister of State for Home Kiran Rijiju had said the cabinet was forced to take the decision because of a constitutional breakdown as six months had lapsed between two sessions of the state assembly.
Following is the chronology of events in the Arunachal Pradesh crisis in which the Supreme Court on Wednesday ordered restoration of the dismissed Congress government by quashing all orders and decisions of the governor taken since December 9, 2015:
Rawat has been called by the CBI to join the probe on Monday, sources said.
Rebel Congress leader Chaudhary Birender Singh on Saturday joined the Bharatiya Janata Party in the presence of its chief Amit Shah at a rally, ending his over four-decade association with the party in poll-bound Haryana.
Another MLA Rekha Arya, who was also supposed to join the BJP on Wednesday, is visiting the Simhasth Kumbh in Ujjain, but has sent her acceptance to the party.
Saket was among the nine members of Legislative Assembly who rebelled against the Harish Rawat government.
A bench headed by Chief Justice Ranjan Gogoi further said Karnataka assembly speaker K R Ramesh Kumar was free to decide on the resignations of the rebel legislators within the time-frame decided by him.
While Nagaraj made no clear announcement of taking back resignation, the same was affirmed by Shivakumar while speaking to media outside Nagaraj's residence.
All 140 MLAs turned up to cast their vote, sources in the legislature secretariat said.
The petition seeking urgent hearing was mentioned before Chief Justice T S Thakur, at his residence, who directed the matter to be listed for hearing on Wednesday.
As the political turmoil lingered on with the ruling coalition making frenetic efforts to win back rebels who have pushed it to the brink of collapse, assembly Speaker K R Ramesh Kumar on Monday announced the confidence motion sought to be moved by Kumaraswamy would be taken up at 11 am on July 18.
A bench headed by the CJI took note of the submission of sr advocate Mukul Rohatgi, appearing for the rebel MLAs.
The Nationalist Congress Party has failed to register even a single win in Pune city with the Bharatiya Janata Party making a clean sweep, winning all 8 seats.
The 10 rebel MLAs had moved apex court alleging that the Karnataka assembly speaker was not accepting their resignations.
Shiv Sena on Wednesday came out strongly against its ally, Bharatiya Janata Party over imposition of President's rule in Uttarakhand
A bench headed by Chief Justice Ranjan Gogoi concluded the hearings of the rebel MLAs, the Speaker and Karnataka Chief Minister H D Kumaraswamy.
The rebel Congress leader said he expressed his desire to join BJP and work under the leadership of Prime Minister Narendra Modi and party president Amit Shah. He also discussed Assam's political and flood situation.
The Supreme Court on Monday refused to pass an interim order on a fervent plea of the Congress against "illegal" swearing-in of its rebel leader Kalikho Pul-led government in Arunachal Pradesh.
Deve Gowda indicated on Sunday that they were ready to compromise.
Nagaraj reached Mumbai accompanied by Karnataka BJP president B S Yeddyurappa's personal assistant Santosh and BJP MLA R Ashok.
10 reasons why the Congress-JD-S government is on the brink of collapse.
The Nainital high court on Wednesday declined the Centre's plea seeking more time to argue Uttarakhand Chief Minister Harish Rawat's plea against President's rule in the state.
Losing power after having come so close, Yediyurappa was determined to regain the reins of power from H D Kumaraswamy.
Union Cabinet met in New Delhi on Saturday night to consider the situation in Uttarakhand amidst speculation that it may consider the option of President's Rule in the state.
In a counter offensive after 13 MLAs resigned on Saturday dealing a blow to the 13-month-old government, a delegation of Congress leaders met Speaker K R Ramesh Kumar and submitted the petition seeking, under the anti-defection law, disqualification of the rebel legislators in line with the decision taken at a meeting of the Congress Legislature Party on Tuesday.
Shankersinh Vaghela claimed Patel's victory in the Rajya Sabha polls came through a 'well thought-out conspiracy'.
Congress members trooped in to the Well of the House raising anti-government slogans.
With the Uttarakhand assembly set to witness a crucial floor test on May 10, a new crisis has risen for former chief minister Harish Rawat in the form of a fresh sting video, which allegedly shows Congress Member of Legislative Assembly Madan Singh admitting to horse-trading.
It also said that there was 'absolute absence of material that would create an apprehension in the mind of the governor' that President's rule needs to be imposed.
The lawyers of the nine rebel Congress MLAs ahead of the trial of strength in Uttarakhand assembly as met Speaker Govind Singh Kunjwal in ab attempt to prevent action against them.
The court also said there was nothing wrong if a no-confidence motion is passed against the Tuki government, which faced a rebellion, in the state assembly when the deputy speaker was in charge of the House proceedings after removal of the speaker.
With Thursday's win, the Congress's strength in the Lok Sabha has gone up to 48.