He said the government should submit evidence in the court instead of revealing everything before the media.
Sena said the police assertion about security threat to Prime Minister Narendra Modi from Maoists was just a "conspiracy theory".
Terming Vajpayee as an "innocent politician" and the "Bheeshm Pitamah", Thackeray said the former PM remained unaffected by ego that comes along with power in politics.
Thackeray made a veiled reference to BJP president Amit Shah writing to the Law Commission, pitching various benefits of holding simultaneous elections to Lok Sabha and state assemblies in the country.
The Sena chief also found fault with the way the BJP was protecting cows, and giving short shrift to women safety.
"Uddhav-ji has asked all party MPs to be present in Delhi tomorrow and they will be told by the Sena president about the party's decision by morning," Harshal Pradhan, a close confidant of Uddhav Thackeray, said here.
"The Ghatkopar incident should be considered as a warning for an impending danger. Mumbai's geography, rising population, cramped and tall buildings needed to be studied with respect to movement of aircraft and their security." Sena mouthpiece 'Saamana' warned.
A senior Sena leader said that Thackeray conveyed it to Pradhan that a meeting was pointless, as an MoU between Saudi Aramco and ADNOC to develop the refinery at Nanar in Ratnagiri has already been inked.
Addressing Sena workers on the party's 52nd foundation day, Thackeray said the BJP spread "lies" ahead of the 2014 general elections and made false promises to people to win the mandate.
Addressing party cadres at Palghar, Thackeray referred to his meeting with Amit Shah yesterday and said, "Whatever is going on now is all drama".
For the BJP, reaching out to allies is crucial to shore up support for the 2019 Lok Sabha elections
Maharashtra Chief Minister Devendra Fadnavis and Uddhav Thackeray's son Aaditya Thackeray were also present at the meeting which lasted about two hours.
The newspaper, which is run by senior Sena leader Sanjay Raut, called Shah and Prime Minister Narendra Modi wilful defaulters in alliance management.
"Winds of change of governance are blowing in Rajasthan and Madhya Pradesh. Change of governance is inevitable in Maharashtra as well. Amit Shah intends to win 350 seats in the Lok Sabha on the BJP's own strength. He says Ram Mandir will be built then. His stubbornness needs to be saluted," the Sena said.
"Amit Shah sought time to meet Uddhavji. Accordingly, an appointment of tomorrow evening has been given to him," Sena MP Sanjay Raut told PTI.
"When the BJP won the Palghar Lok Sabha seat in 2014, the victory margin was of lakhs of votes. Today, they barely managed to win by a few thousand votes," Thackeray told reporters here, after his party's candidate lost the Palghar Lok Sabha bypoll.
The Sena president demanded that "cases" should be filed against those demanding separate statehood for Vidarbha.
Sena, ally of the BJP in the Centre and in Maharashtra, continually takes swipe at the the prime minister and his party, especially through its mouthpiece 'Saamana'.
Speaking at the release of Marathi book Gof, penned by Sena's Rajya Sabha MP and Saamana executive editor Sanjay Raut, Thackeray directly addressed RSS leader Sunil Deodhar, who is credited for the BJP's victory in Tripura Assembly elections.
“Shiv Sena will do everything according to its own schedule,” said Thackeray late on Thursday evening, in reaction to the rift between BJP and its NDA ally TDP.
NCP spokesperson Mahesh Tapase said here that while the entire political class praised the interview, Uddhav Thackeray did not do so, which shows he was nowhere close to his "large-hearted" father late Bal Thackeray.
Thackeray said there was an atmosphere of suspicion towards banks in the country today
"The decision of those judges should be lauded. There is a high possibility that there will be an inquiry called against them now. However, this inquiry should be unbiased," Thackeray told reporters here.
Speaking at a function in neighbouring Navi Mumbai, the Sena chief said that some "invisible hands" had a role in playing caste politics in the state.
Uddhav Thackeray took charge as the party president on January 23, 2013, after the death of his father Bal Thackeray (86) in November 2012.