Midfielder Corentin Tolisso suffered anterior cruciate ligament damage against Bayer Leverkusen on Saturday while Rafinha damaged his ankle ligaments after a tackle from Karim Bellarabi, who appeared to stamp on his heel.
Bellarabi was sent off after the challenge, with Rafinha due to be out for a "number of weeks", while Tolisso will miss several months.
The Bavarians are already without Kingsley Coman until 2019 after he suffered an ankle ligament injury in August, leaving them with just 16 fit outfield players to see them through the first half of the campaign.
Bayern president Uli Hoeness claimed that Bellarabi should be handed a three-month ban after his "assault" on Rafinha and Kovac has echoed those sentiments, maintaining that referees have a duty to protect players.
"I've always been someone who said that football is a contact sport," he told Goal in an exclusive interview.
"It's part of it, but you also have to watch out for the health of the players.
STOMP!— Goal (@goal) September 16, 2018
Did Karim Bellarabi deserve to be sent off for this? pic.twitter.com/1VeeDQdCA0
"When it comes down to the bones or joints, you have to find sanctions much earlier - be it yellow cards or more, it cannot be that we're losing players all the time. I'm talking about Bayern Munich, but there are other clubs, too, of course.
"There really has to be consideration for the players."
And Kovac - who joined the club from Eintract Frankfurt over the summer - is confident that perfect start can continue, despite his depleted squad.
"Of course I am very sad, disappointed and sad," he added.
"Tolisso will be out for a long time, Rafinha returns a little faster. We have a very small squad and now two players are seriously injured and Rafinha is injured as well.
"Now we have to complete the upcoming games with a reduced number of players. This is annoying, of course. But we must not complain now, because we have the quality to do it nevertheless."