President Barack Obama acknowledged Friday that there are “long-term issues” facing the Veterans Affairs Department in wake of the scandal ensnaring the agency that led to the resignation of Secretary Eric Shinseki.

At a news conference Friday announcing his acceptance of Shinseki’s resignation, Obama said the retired general and Rob Nabors, the president’s deputy chief of staff, made a presentation of the department’s initial review of VA facilities across the country.

“And what they found is that the misconduct has not been limited to a few VA facilities, but many across the country. Totally unacceptable. Our veterans deserve the best. They’ve earned it. Last week I said that if we found misconduct, it would be punished, and I meant it,” Obama said, according to a transcript of the announcement.

Obama said the department is facing “long-term issues” that came to light from the scandal. In the case of the Phoenix VA hospital, some veterans have had to wait as much as six months before their first appointment. Officials at the hospital were found to have put the veterans on a secret waiting list that they were never notified about in an attempt to make its wait times appear shorter than they actually were.

The president said there needs to be a “change of culture” at the VA, including being more forthcoming about bad information like the wait times in Phoenix. But he said the source of that problem is something that can be “tackled right away.”

“Everybody who’s out there waiting, get them an appointment,” Obama said. “The challenge is getting veterans into the door for their first appointment, in some cases.”

Obama said Shinseki started firing people responsible for problems at the Phoenix VA, including senior leaders, and that the hospital will personally call every veteran who has struggled to get an appointment. Senior executives of the department have also had their performance bonuses canceled, the president said.

Deputy Veterans Affairs Secretary Sloan Gibson will be taking over as acting secretary.