The former England, Liverpool and Manchester United striker, who retired at the end of last season aged 33, is concerned that young players are stopped from experiencing tournaments at age-group level.
England Under-20s and Under-21s both failed to make an impact in major tournaments this summer. Stuart Pearce's Under-21s crashed out of the European Championship in Israel - with Pearce's contract not being renewed as a result - while Peter Taylor's winless Under-20 side finished bottom of the group stage in the World Cup in Turkey.
Jack Rodwell, Alex Oxlade-Chamberlain and Phil Jones were all eligible for the Under-21 tournament but were instead called up for the senior side's international friendlies against Ireland and Brazil.
And Owen, in comments which echo ones made by Rio Ferdinand last month, believe denying the age-group sides their best players for the senior team is not the best strategy.
"I worry about the future of our national team," Owen told Sportlobster.com.
"Of course, the obvious excuse is to say we were missing some of our best young players as they were in the senior squad.
"This was certainly the case but it's worrying that our senior team apparently needs them so much that our young national teams have to suffer in such a way.
"Excuses aside, the truth is that we're falling short of the level expected at present and I'm concerned about the future of all our national teams."