The FIR filed against Amit Shah on Sunday for making a speech laced with anti-Muslim references isn't the only problem the Bharatiya Janata Party faces from its controversial general secretary. The party's Uttar Pradesh unit is also feeling the effects of the tensions simmering between Shah and party president Rajnath Singh.

Since May, Shah has enjoyed a free hand in the party’s affairs in UP as he pursues his ambitious project to ensure victory in the state. With 80 Lok Sabha seats, Uttar Pradesh is the vital hurdle Narendra Modi must cross if he is to become Prime Minister. In each of the last two elections, the BJP has won merely 10 seats in this state.

Shah has been given complete charge of the BJP machinery. Having proved himself as Modi’s right-hand man in Gujarat, where he served as home minister, Shah is supervising the UP campaign down to the smallest detail.

But now that Shah is driving the party in UP, a sense of loss seems to have started dawning on BJP president Rajnath Singh, who has spent more than four decades helping the state unit of the party to grow in strength. The unusually high stakes for the BJP in the general election have stopped the unease between the men from spilling out, but the strain between them has begun to show up occasionally.

One of those occasions came last week, when Shah told media persons that the party would not change any of the candidates it has announced in UP, except for perhaps Fatehpur Sikri. “We are thinking over that seat,” he said.

On the face of it, Shah’s statement appeared to send a clear signal to disgruntled elements in the party that dissent would not be entertained.

However, BJP members who declined to be identified said that the statement was actually aimed at derailing a concerted last-minute effort by Rajnath Singh to reclaim this authority in a state he considers his own.

Rajnath, who is considered the BJP’s topmost leader in UP, had his first inning as the BJP president in December 2005, but his term was marked by internal squabbles. Few would have predicted a second stint for him, but he had a second chance in January 2013, after Nitin Gadkari was forced to resign from the position following an income-tax raid into dubious investments in a company controlled by him. Right from the beginning of his second term, Rajnath was a vociferous backer of Modi. In fact, he himself paved the way for Shah’s entry into UP. However, he probably underestimated the extent to which Shah would try to alter the power equations in the state BJP unit.

In Fatehpur Sikri, which has a substantial Thakur population, the BJP is up against Amar Singh of the Rashtriya Lok Dal. As a Thakur himself, Rajnath believed he would have the right to choose the candidate for this seat, and also a few others. Babulal Choudhary, the candidate picked by the BJP, is a Jat.

Udaybhaan Singh, a prominent BJP Thakur leader, who is close to Ranjanth, has been rearing to contest this seat. In fact, he has threatened to run as an independent if party refuses him ticket.

“Besides Fatehpur Sikri, there are four or five other seats in which Rajnath Singh wants his men to get tickets,” said a senior BJP leader on condition of anonymity.

By conceding the demand to change the party candidate in Fatehpur Sikri while remaining adamant on all other seats, Shah may well be offering a compromise to Rajnath.

It is not that Rajnath had no say in ticket distribution in the state. He is considered to be close to Modi, and Shah could not have overhauled the party in UP without his blessings. It is also true that many of those considered close to Rajnath have been duly accommodated in the candidates’ list. Despite this, several Rajnath loyalists have found themselves in the cold, party officials said on condition of anonymity.

In fact, one of his Rajnath's aides, Ramapati Ram Tripathi, who feared uncertainty in the distribution of tickets under the supervision of Shah, spent ten days in Delhi at beginning of March when the election committee of the party was finalising the first list of 53 candidates for Uttar Pradesh. Despite this, he initially failed to get the name of his son, Sharad Tripathi, an aspirant from Sant Kabir Nagar constituency, included in this list, party officials said. “Only later, after much efforts by Rajnath, could Sharad managed to get party’s ticket from Sant Kabir Nagar constituency,” a BJP leader said.

Officials said that the unusual delay in finalising the subsequent lists of candidates in UP was the result of Rajnath’s late realisation that many of his loyalists had not been given tickets. While party took hardly a week to finalise nearly two-thirds of its candidates for UP, it had to deliberate for over three weeks over the other party nominees, announcing the names only by the end of March.

It is yet to be seen whether Shah’s experiments will actually deliver his aim: to win more than 40 of UP’s 80 Lok Sabha seats. What is certain, however, is that these experiments are now threatening to weaken the network of loyalists Rajnath has cultivated so assiduously over long decades.

From Rajnath's point of view, the stand off is significant. It will become even more so if Modi wins both Varanasi and Vadodara seats, but decides to retain the UP seat. According to BJP officials, the chances of Modi doing that are very high because control over the state is crucial for anyone wanting to have a grip on the country’s most powerful office. Besides, in the event that UP does not throw up enough seats for the BJP, Rajnath would be left with a party unit more difficult to control than ever before.