Referees have been told to remind players of the need to maintain social distancing as much as possible during games, and when celebrating goals.
Speaking after City's win over Brighton on Wednesday, in which Phil Foden scored the winner and celebrated with the majority of his team-mates, Guardiola admitted it is "difficult" to follow the protocols as celebrating is an "instinct".
"We will follow what the Premier League says but I don't know if we will be able to do it," said Guardiola.
"I respect the Premier League protocols. I understand completely what they are trying to do. When we are indoors everyone respects social distancing. We have to do it. But outdoors, on the training pitch, after being tested many times, in the real moment of joy, [hugging] is instinct and reaction. It is difficult. I don't know if we will be able to do it."