He claimed the NDA government bought the planes at Rs 1,600 crore a piece as against the Rs 526 crore for each aircraft fixed by the UPA.
He also advised Congress chief Rahul Gandhi to "learn" from former defence minister Pranab Mukherjee "lessons on national security."
"It is reiterated that the petitioners are using documents with the intention to present a selective and incomplete picture of internal secret deliberations on a matter relating to national security and defence," the defence ministry said.
The top court had rejected the objections raised by the Centre that those documents were not admissible as evidence under Section 123 of the Indian Evidence Act, and no one can produce them in court without the permission of the department concerned as they are also protected under the Official Secrets Act.
Defence Ministry says the report is being verified, maintaining that neither Indian nor French government had any say in the decision.
A day after Defence Minister Rajnath Singh formally took delivery of the first of the 36 Rafale multi-role fighter jets, Dassault Aviation, the French company that manufactures the jets, has released the first airborne photographs of the second aircraft with the tail number RB-002.
He also called out Defence Minister Nirmala Sithraman for changing her stance on revealing the cost of Rafale.
He also cautioned against politicisation of defence purchases, suggesting that this had earlier led to the delay in the army acquiring the Bofors gun.
Referring to Modi's speeches in Parliament on Wednesday, he said it was clear that the prime minister was not interested in answering "fundamental questions".
Dhanoa is a on a four-day visit to France to ramp up cooperation between the air forces of the two countries in a range of areas.
Macron, who assumed the presidency in May 2017, emphasised that this is a government-to-government discussion and "this contract is part of a broader framework which is military and defence" coalition between India and France.
The court's remarks came when the petitioner said they were seeking a court-monitored CBI probe into the deal.
The apex court at the same time made it clear that it does not want information on pricing and technical parameters relating to the fighter aircraft.
Rahul Bedi explains how 'miscellaneous' factors have posed a major hurdle in negotiating the Rafale deal.
Addressing a press conference in the nation's capital, he claimed that Verma's removal was an "insult" to the Constitution, the chief justice of India and the leader of the opposition.
The trio also accused PM Modi of single-handedly changing the parameters of the deal.
Oppn members raised slogans demanding a joint parliamentary committee probe into the issue.
Congress said it expects the truth to prevail after the report on the Rafale deal is made public.
Gandhi claimed that Modi will not be able to look him in the eye if the two debate the Rafale deal.
With the Rafale fighter deal stuck over price negotiations, can the prime minister step in and find a way out for both countries?
Rahul targets the Modi government on Twitter, using the hashtag "BikGayaChowkidar".
MoD dismissed the report saying it draws 'conjectural connection between tax exemption to a private company and procurement of Rafale jets'.
There is considerable discomfort within the defence ministry about the Rafale deal.
The debate on the Rafale jet fighter deal saw a head-on collision between the government and the Congress in Lok Sabha on Wednesday.
The report noted that the 2007 UPA deal included a 15 per cent bank guarantee against advance payments.
The Congress, which was not a petitioner before the apex court, wants the Rafale deal to be referred to a Joint Parliamentary Committee to go into the price arrived at by the BJP government versus the one negotiated by the previous UPA regime, as also how billionaire Anil Ambani's group with virtually no experience in manufacture of fighter jets was selected as an offset partner for the deal.
An internal document shows Dassault Aviation considered Reliance offset deal as a 'trade off' to clinch Rafale deal'.
Randeep Surjewala also accused the government of "doublespeak" and "sacrificing" national interests.
The Supreme Court's verdict on the Rafale deal spurred a war of words between the BJP and the Congress.
The Congress president had on April 10 claimed that the apex court has made it "clear" that Prime Minister Narendra Modi "committed a theft".
The Congress has launched an offensive against the Bharatiya Janata Party government over the Rafale deal, alleging corruption and violation of rules by Prime Minister Narendra Modi and demanded answers from him.
The apex court on December 14 last year dismissed a clutch of PILs, including the one filed by former Union ministers Yashwant Sinha and Arun Shourie and lawyer Prashant Bhushan, saying there was "no occasion to doubt" the decision-making process of the Centre in the procurement of 36 Rafale jets from France.
Gandhi's attack came a day after Defence Minister Nirmala Sitharaman had refused to share the details of the deal on the grounds of security agreement signed between India and France.
Congress vice president Rahul Gandhi on Sunday hit back at Defence Minister Nirmala Sitharaman over the multi-crore Rafale deal, claiming it was "shameful" that her boss was "silencing" her.
"How many more lies will be peddled to sustain a sinking dynast? India, certainly deserves better," Jaitley said.
Shiv Sena leader Sanjay Raut on Wednesday termed the Maharashtra governor's order asking the Uddhav Thackeray-led government to prove its majority in the assembly as "unlawful", saying that the Supreme Court is yet to decide on the disqualification of 16 rebel MLAs.
"We are little perplexed that the two cases are listed on two different dates when the order was that these matters will be heard together," the bench said.
The petition by the trio came two weeks after the apex court had on October 10 asked the Centre to provide details of the decision-making process in the Rafale deal with France in a sealed cover by October 29.
India's multi-billion dollar Rafale fighter jet contract with France continues to be stuck in the doldrums even as the two countries have agreed to "fast-track" the negotiations.
Two former union ministers have sought registration of an FIR into the fighter jet deal between India and France alleging "criminal misconduct" by high public functionaries.
