"It's no secret, this hasn't worked well enough - far from it," Löfven said at a press conference on Friday afternoon.
"The nomination process showed negligence and that's unacceptable. A party needs to stay organized."
Löfven's comments come following a storm of controversy, which began when Omar Mustafa was chosen to sit on the governing board of the left-of-centre opposition party at last weekend's party congress.
Mustafa also acts as the chairman of the Islamic Association (Islamiska förbundet) in Sweden, a group which has invited speakers to Sweden with known anti-Semitic views - a fact that emerged just days after Mustafa was elected to the party's governing board.
Mustafa publicly distanced himself from all anti-Semitism and racial agitation. However, it wasn't enough for Löfven who issued an ultimatum which led to Mustafa's departure on Saturday, with the ousted board member claiming he was "forced out".
At the press conference on Friday, Löfven explained that the Social Democrats had zero tolerance for anyone not sharing the party's values.
"There can be no uncertainty, if you represent our party you have to stand up for our values," he told reporters.