ELDC leaders, however, were not concerned by the news as the authority voted 33 for and 11 against to pass the agreement which should see £15.4m saved over 10 years.
Following a vote to approve the latest move at Full Council last night, the alliance officially came into effect today (July 1).
It will see the two councils sharing Chief Executive Rob Barlow and other senior officers as part of a wider move to join workforces over the next few years.
Both authorities have been keen to say the move is not a merger, and that they will retain their own identities.
Boston Borough councillors opposed to the plan, however, have issued a barrister’s letter to the authority’s leader setting out their “grave concerns” and threatening a judicial review if they are not addressed.
They said they were not opposed to an alliance in principle, however, “we simply cannot support this alliance in its current form.”
“Despite asking for answers to our many legal, financial and procedural questions, we have received absolutely no response from the ruling group at this council,” said the councillors.
They said the barrister, Simon Bell, was recommended by the Local Government Association and had already offered advice.
“There is no doubt that the proposed Strategic Alliance has been rushed through our council in a matter of weeks,” said the statement.
“Our questions about staffing, finances, processes and procedures have fallen on deaf ears, and this left us with no choice but to seek a remedy elsewhere.”
During ELDC’s meeting Councillor Andrew Leonard, who had been told of the move beforehand, said: “I don’t think we should be voting on anything tonight, in fact I think this whole meeting should be deferred. They’ve engaged a barrister.”
“It doesn’t stand and (one councillor has) described it as a complete fiasco, the whole thing is invalid and we shouldn’t be moving forward until we know what their final decision is... they’re adamant they’re going to be looking to a judicial review.”
He added concerns that when deputy leader of Boston Councillor Nigel Welton withdrew the alliance following initial difficulties, he did so without a seconder to the motion.
However, East Lindsey District Council leader Craig Leyland said: “Judicial reviews have to be judged on their quality and for us not to proceed tonight on the basis of a judicial review, written and not actually understood, would be foolish.”
Councillors sought reassurance over incomplete information, redundancy payments, scrutiny, and the impact if either council chose to withdraw at a later point.
In a joint statement following the meeting, Cllr Leyland along with Boston Council leader Paul Skinner said: “Though we have always worked closely, a formal partnership will strengthen both organisations as we seek to deliver our growth ambitions and look to overcome future challenges.
“By working closer together, we will be able to continue to deliver the services our residents expect in a more efficient and innovative way.”