The U's survival hopes look slim as they currently sit 10 points from safety with six games to go.
"It's all very well me sitting here saying I know who I want to keep," Keen told BBC Radio Essex.
"There will be a lot of external influences throughout the summer depending on what league we're in."
Colchester are unbeaten in their last three games and travel to 20th-placed Blackpool on Saturday.
"It's very difficult for me to say 'I want to keep him, him and him, those contracts are sorted and we're all good for next year,'" added Keen. "I can't see a scenario where that's going to happen.
"I can see a scenario where players in contract will be sought after by other teams. Players out of contract will have choices to make.
"There are very good players in contract, so we'll just have to wait and see what happens in the summer."
Colchester boss Kevin Keen says it is very difficult to persuade players to commit to the club until they know what league they will play in.