Lofven was pushed to take action when Alliance, the opposition coalition, moved a motion of no-confidence against Ygeman, Johhansson and Hultqvist.
According to Expressen, sensitive information including the entire registry of Swedish drivers' licenses and data on protected identities was accessible to people who had not been vetted by the Swedish security service.
The Transport Agency offered its assurance that, to its knowledge, none of the vulnerable data outsourced to IMB had landed in the wrong hands.
Sweden is in the grip of a political crisis as Prime Minister Stefan Lofven reshuffled his minority cabinet in a bid to avoid calling an early election.
The leak of classified information is said to stem from the Swedish transport agency's outsourcing to IBM in 2015 to manage its IT databases and networks.
It remains to be seen whether Alliance will continue their efforts against the Defence Minister.
"I don't want political chaos", he said. Lofven, who described the incident as a disaster that put Sweden and Swedes in harm's way, said he first heard about it in January, some 18 months after the leak occurred. "It wouldn't serve Sweden to throw the country into a political crisis".
The Swedish Prime Minister labelled the no confidence motion against Defense Minister Hultqvist as "completely irresponsible".
On Thursday afternoon, the opposition Alliance parties jointly announced they would push forward with their no confidence motion against Hultqvist.
The leader of the centrist Christian Democrats, Ebba Busch Thor, and the leader of the far-right Swedish Democrats, Jimmie Akesson, said on Twitter they would support the motion.
"Sweden's security has been jeopardised".