Tottenham 's Kane suffered a ruptured tendon in his hamstring which required surgery, while Manchester United forward Rashford sustained a double stress fracture of his back.
“I'm so sorry for Kane and Rashford, but we demand a lot from the players, it's too much," said Guardiola.
“The players deserve to be treated as they should be, so they perform as well as possible.
“It's unsustainable. The players fall down. It's too much. They [the authorities] should reflect on it but all the managers complained about it and they don't care.
“The players suffer. We push and push, but the body says stop, it's enough. Of course it's too much to expect.
“The players arrive at the Euros, playing with the national teams, trying their best, then back here after no more than 20 days because the business, the show must go on.
“The big administration people cannot complain, because it's normal this happens.
“With that number of games, players break down. I'm not surprised. I'm so sorry for them."