Denmark international Eriksen has been an influential figure in Pochettino's side that finished runners-up to Liverpool in the Champions League and were fourth in the Premier League last season.
The 27-year-old midfielder, whose contract will end after the current campaign, has said he wanted a new challenge. He has been heavily linked by the Spanish media with a move to Real Madrid before the European transfer window closes on September 2.
"It's not the best situation for him (Eriksen) and for everyone," Pochettino told reporters.
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"It is not what I think the club or the player expected (it) to be. You cannot put a finger on the problem.
"You try to minimalise the problem, try to treat the situation. This is an important player who needs to help the team with his performances."
Pochettino would like Eriksen to continue to be part of his squad but the club may need to consider offers for a player who could leave for free at the end of the season.
"I am always open to help the club and to help the decision of Daniel (Levy)," Pochettino added.
"I know really well that decisions like this are not easy but I always try to be in the position to take the best benefit for the club."
Eriksen is set to feature for Spurs in Sunday's league clash against Newcastle United, with record signing Tanguy Ndombele out with a minor thigh injury and Giovani Lo Celso lacking match fitness.
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