Slot's remarks came after the Swedish striker, who completed a British record 125 million pounds ($168 million) move to Anfield following a summer-long transfer tussle, suffered a groin injury.
Slot had previously said: "You cannot compare a player who maybe hasn't trained or played in pre-season for a smaller club to then go to Liverpool."
Isak was frozen out of the Newcastle squad and trained alone while awaiting his Merseyside switch.
Isak, who has yet to score for Liverpool in the Premier League or Champions League, suffered a setback when he came off in their midweek win over Eintracht Frankfurt and is a doubt for the weekend.
Although Slot's comments did not sit well with Newcastle fans, the club's manager did not engage.
"I don't think that's wise for me to get involved in those discussions. Alex is no longer at this football club, so I won't comment on it," Howe said when pressed by reporters on Friday, ahead of Saturday's home game against Fulham.
"I think the set-up (training facilities) here is very good. It's not perfect. We've got things to improve and to grow, but the club and the owners here have developed the facilities since I've been here very, very well.
"You can see there's building work going on currently to hopefully help us deliver even better in the future. But I've got no complaints. We've got elite athletes here, many of them."
Howe pleased with Woltemade
While Liverpool grapple with their expensive acquisition's early struggles, Newcastle appear to have found a gem in Isak's replacement Nick Woltemade, who has hit the ground running with five goals in all competitions.
"Physically there has been a vast improvement (since his arrival)," Howe said.
"The challenge for him at this moment is that he's got to do it every three or four days and that is not easy physically and mentally. He has a lot of responsibility on his shoulders but he is carrying that really well.
"I see a player and a person coming into the training ground that feels more at home in his environment, a lot more relaxed and you are seeing his natural personality come out. I am very pleased with him."
However, Newcastle's other forward signing Yoane Wissa faces a longer road to fitness after sustaining an injury on international duty, with the striker yet to play for the club since his move.
"He will need almost a pre-season and the pre-season schedule we give to players is six weeks," Howe said.
"We do that for a reason so we can build them up. I'm not saying he won't play for six weeks but to get to his very best level it will probably take that time."