The JDU, in alliance with the BJP, will contest two seats in the February 8 Delhi election.
Janata Dal (United) leader Vashishtha Narayan Singh on Wednesday criticised party leader Pavan Varma for questioning "in public" the BJP tie-up for the Delhi assembly polls, calling it "absolutely" an act of indiscipline.
Mr Singh, a Rajya Sabha member and the head of the JD(U) state unit, said the decision to align with the BJP was taken after "due deliberation".
He said although the party respected freedom of thought of every member, it was "anuchit" (inappropriate) on part of the career diplomat-turned-politician to make public his letter to the Chief Minister and national president Nitish Kumar.
The JDU, in alliance with the BJP for the first time in Delhi, will contest two seats in the February 8 election.
In a letter to Nitish Kumar, Pavan K Varma had said he is "deeply perplexed" by the development amid the citizenship law protests and is looking to him for "ideological clarity".
"I consider his (Pavan Varma) conduct as inappropriate and will put forth my views forcefully whenever a party meeting takes place", Mr Singh said.
He said "if there were any reservations, these ought to have been expressed in a party forum. People may have their individual opinions and the party respects that. But airing these in public is something I do not approve of".
"On more than one occasion, you have expressed your grave apprehensions about the BJP-RSS combine," Pavan Varma said in the letter on Tuesday.
"If these are your real views, I fail to understand how the JDU is now extending its alliance with the BJP beyond Bihar, when even long standing allies of the BJP, like the Akali Dal, have refused to do so," he wrote.
On Monday, the Akali Dal, the BJP's Punjab ally, opted out of the Delhi polls citing reservations over the Citizenship (Amendment) Act or CAA. The Akali said the exclusion of Muslims from the law was not acceptable to it.
Meanwhile, the opposition RJD came out in support of Mr Varma's demand for "ideological clarity" by Nitish Kumar.
RJD vice-president Raghuvansh Prasad Singh said: "Ideological clarity is needed since Mr Kumar has left his own party colleagues confused
as to where he stands on the most burning issue of the day."
"Pavan Varma is not alone. Prashant Kishor (JD-U national vice president) seems similarly bewildered. (Nitish) Kumar got his party to support CAA in Parliament and on the other hand says he is stoutly opposed to NRC. This is irreconcilable", he added.