Tottenham striker Kane scored just 79 seconds into his senior international debut in a 4-0 victory over Lithuania on Friday, taking his tally to 30 goals for the season in all competitions.
England face a friendly against Republic of Ireland and a Euro 2016 qualifying clash with Slovenia while the under-21s are in the Czech Republic, but youth boss Southgate is confident of having Kane at his disposal.
"Roy and I know that the seniors are in a good group position and he feels that the experience of going to the Czech Republic in the summer will be more beneficial to Harry than the two games he has got," he said.
"That is absolutely the case regardless of his displays between now and then.
"We are not short of good players in the seniors but understandably for Harry to be there this time, against Lithuania, was merited.
"We still feel we can give the players the best possible preparation to go into the seniors and achieve success if they have got the experience of the European Under-21 Championship behind them. That is still the case with Harry."
