Sharad Pawar, who heads the second-largest member of the Congress-led coalition government, called Prime Minister Manmohan Singh and expressed his opposition to appointment of a judge at this juncture to probe the issue.
Jammu and Kashmir Chief Minister Omar Abdullah, whose National Conference also participates in the government, tweeted, "Was talking to my dad last night & he felt the same way - setting up a commission of inquiry in the dying hours of UPA 2 is just wrong".
Modi came in the line of fire after it was alleged that illegal surveillance was carried out on a young woman in Gujarat in 2009 at his behest as Gujarat Chief Minister, as also Amit Shah, who was then the state's Home Minister.
Government announced on Friday that a judge would be appointed by May 16 to probe the issue, drawing the ire of the BJP.
Notwithstanding the opposition by NCP and NC, Congress made it clear that the judge will be appointed, asserting that there will be "no compromise" as the issue involved women of the country.
BJP today welcomed the stand taken by the two UPA allies, saying even coalition partners are refusing to be part of Congress's "politics of vendetta".
"It shows that UPA allies have found sense. They are seeing the truth. This is the politics of vendetta which is the speciality of Congress. Political parties do not want to get involved in it," BJP national spokesperson M J Akbar told reporters here.
Union Minister and senior NCP leader Praful Patel told PTI, "When the results of the Lok Sabha elections are due in two weeks' time, where is the need for such an enquiry."
Striking a similar note, Omar said if the decision to appoint could not be taken in December then it was wrong to appoint a judge five months later.
"If the decision to appoint a commission was taken in Dec it should have been implemented. To appoint a judge 5 months later is wrong," he tweeted.
The statements came close on the heels of Home Minister Sushilkumar Shinde and Law Minister Kapil Sibal insisting that government planned to go ahead with naming a judge for the enquiry before May 16, the day on which Lok Sabha election results will be out.
Unfazed by the opposition from its two allies, Congress spokesperson and Mahila Congress chief Shoba Oza asserted that there will be "no compromise" on going ahead with the probe as the matter concerns women of the country who constitute half of the population.
The party also came out with 10 questions to BJP including Modi, Amit Shah and Arun Jaitley on snoopgate controversy, asking them to "come clean" on the issue.
Union Minister Salman Khurshid said the allies' views can be discussed within the government.
"This is something which we can discuss within the government. There can always be different points of view and at the end of the day you take a call," he said.
BJP slammed the Congress for alleging that the girl involved in the case had been bought by the Gujarat government to stay silent, and said "no one is in the market to purchase Congress's lies anymore".
"When lies become a habit, then you can just keep on spinning off lies. All I am trying to say and there is evidence before you that no one is in the market to purchase Congress's lies anymore. Not even those who have been with the Congress for 15 years," Akbar said.
He said that those who kept the UPA alive too are asking the Congress to stop "politics of filth" and get back to the politics of issues.