Robert Abela has admitted there are "differences of opinion" within Labour with the party's CEO Randolph De Battista.
The prime minister said he would not be removing De Battista from the party's parliamentary group but refused to give the same assurances about his role as chief executive.
Following a meeting between the pair on Wednesday, De Battista said he will stay on in the role.
"But the important thing is not whether I'm still there or not, because anyone who knows me knows that I don't like to talk about myself or the work I'm doing in my role which is to see that the Party's finances are managed wisely," he said.
Questions over his position emerged following a meeting of the Labour Party's executive and parliamentary group where Abela blamed ineffectual party administration for its dismal performance in the European elections.
"Randolph is an integral part of the (parliamentary) group. He has opinions that are not necessarily the same as that of all who are in the Labour parliamentary group," Abela told Times of Malta in a doorstep on Wednesday morning.
"Do I agree with him on everything? No," Abela said.
He said that some of De Battista's opinions might reflect the message sent by the electorate, which reduced Labour's majority over the PN to just 8,500 votes from 42,000 in the 2019 election.
Abela said he would not be censoring or eliminating De Battista as an MP but when asked about his CEO role, the Labour leader said: "That is a discussion we need to have and to respect that discussion I would rather not comment".
Meanwhile, De Battista said his future was in the hands of the prime minister but added that as CEO his role was to keep the financial and administrative situation of the party sustainable.
"I always worked genuinely in that regard" he said.
He said there were certain issues that he had always raised internally but that now he was "happy that others are also speaking about those issues."
Abela was also asked about his confidence in housing minister Roderick Galdes.
During Monday's joint parliamentary and executive group meeting Galdes was given a "dressing down".
One MP said Galdes was criticised over people around him failing to show respect for those asking for services for the ministry.
However Malta Today reported that Galdes was also singled out for criticism over being the minister responsible for a debacle in Siġġiewi that saw magistrates reversing an order to register 99 voters in unfinished flats ahead of the election.
But on camera, Abela praised Galdes.
"There is not only trust in him as a minister but also a personal friendship that goes back many years," he said.
Abela said he spoke generally in the meeting and appealed for more sensitivity when encountering people's realities and challenges.
"Its not an issue of favours, its an issue of their rights. When people speak to us about their rights we need to be sensitive to their realities" he said.
In issues like health, housing or social benefits there needs to be a certain sensitivity, he said.