Thackeray said that he respected Modi for having improved Gujarat's economy, but as someone aspiring to lead the whole country, he ought to have given up his regional role.
"A lot of nationwide changes are called for," Thackeray told reporters in Nashik, north of Mumbai, following a meeting of all state legislators from his party. "It isn't right for him to devote his energies to one region."
Thackeray criticised Modi for praising Sardar Patel, a leader from Gujarat in the Indian independence movement, when on a visit to Mumbai, but not Chhatrapati Shivaji, the warrior king who is a hero of Maharashtrians.
These comments came two days after Modi visited Raigad district and made positive statements about Shivaji.
While not especially harsh in themselves, this is the first time that Raj Thackeray has been critical of Modi, with whom he has shared a warm personal rapport.
But his statement isn't surprising. In October, after several months of uncertainty, the Bharatiya Janata Party reaffirmed its two-decade alliance with the Shiv Sena, headed by Raj Thackeray's cousin Uddhav Thackeray. Raj Thackeray had split from the Shiv Sena in 2006 to form his own party.
The alliance, which is the main opposition in Maharashtra, also managed to rope in the Republican Party of India (Athavale) late last year. Two days ago, it was joined by the Swabhimaani Shetkari Sanghatana, a party with clout in rural western Maharashtra that is led by Lok Sabha member Raju Shetti.
This prosperous region is the traditional stronghold of the Nationalist Congress Party, which is part of the ruling coalition in Maharashtra. The alliance, which does not have much of a following in this region, has much to gain from Shetti's network.
Raj Thackeray told reporters on Thursday that he had no intention of joining this alliance. He could not have even if he wanted to.
Devendra Fadnavis, the head of BJP's state unit, was caustic in his response to Thackeray's statements. "We don't need advice about what Modi should or should not do," he told news channels. "He has been going around the country with lakhs of people attending his rallies. If people can't stomach his success, then that is their problem."
While the BJP may have been once toying with the idea of including Raj Thackeray's party in the alliance by attempting a reconciliation between the two estranged cousins or even severing its ties with the Shiv Sena and going just with Raj Thackeray's party, this is clearly no longer the case.
The BJP had been trying to forge a grand alliance of right-wing parties in Maharashtra in the hope of defeating the Congress, which has been in power in the state since 1999 and has become increasingly mired in corruption scandals, both nationally and in the state.
The BJP-Shiv Sena alliance has been in power only once in the state, winning the election in 1994. Maharashtra has 48 Lok Sabha seats, and by expanding its alliance, the BJP hoped it could win more seats than the Congress-NCP alliance in the general election due later this year and win a majority in the state election due afterwards.
Now, however, Raj Thackeray does not have a reason to be careful about what he says about the BJP or Modi.
Another reason Raj Thackeray might have been emboldened is the Aam Aadmi Party factor, said Surendra Jondhale, a professor of political science at the University of Mumbai who is a close watcher of Maharashtra politics.
"The AAP's stunning results in the Delhi assembly election has shown people that no one is invincible, including Modi," he said.
In contrast with Raj, his cousin Uddhav Thackeray has had frosty relations with Gujarat's chief minister, a fact that had earlier last year threatened to undo his party's two-decade alliance with the Bharatiya Janata Party.
In July, while on a visit to New Delhi, Uddhav Thackeray, made a jab at Modi by saying that while Indian needed a strong government and credible leader, he did not see anyone who fit that description.
He made this statement at a time when it was clear to everyone that the BJP was on the verge of announcing Modi as its prime ministerial candidate.
Raj Thackeray may have also realised that not being part of a BJP-Shiv Sena alliance might actually help him to preserve his party's political identity, Jondhale said.
Now that he has to go it alone, he might as well make the most of it and carve an independent space for himself, especially by the time the state election comes around, he said.
In response to a question, Nitin Sardesai, spokesman for the Maharashtra Navnirman Sena, told the Marathi news channel IBN Lokmat on Thursday night that Raj Thackeray was not an agent of the Congress and that he had an independent role to play in the state's political sphere.