Allen will play for Wales against Bosnia on Wednesday despite his Olympics campaign.
Rodgers said: "I had a chat with Chris Coleman. I've spoken to one or two of the international managers - including Roy [Hodgson] and the Denmark manager.
"It's not for me to tell these guys how to do their jobs but I think they all understand this type of game and the time of it.
"We hoped Joe could play against Leverkusen but he couldn't. If he gets 45 to 60 minutes (for Wales) it won't hurt him."