England midfielder Jack Wilshere ignited the debate over the naturalising of players for the international team, sharing his belief on Tuesday that only home-grown footballers should be eligible.
Wilshere was speaking in the wake of the FA looking at the possibility of Januzaj becoming available for England in years to come.
The Belgium-born winger is available to play for the country of his birth, Albania, Kosovo, Serbia and Turkey, while if he remains in England for the next five years he could represent the national team in 2018 on residency grounds.
Januzaj would be 23 before he was England-ready, and Bernstein has no problem with the FA looking at all their options, given other countries may be doing the same.
"We live in a changing world where there is much more fluidity in terms of population movements," Bernstein told BBC Radio Five Live.
"I'd say we must play within the rules obviously, but if within the rules there are players who are eligible to play for England I would be inclined to pick the best players we can get.
"Other countries do that and we want to be on a level playing field doing that.
"I would prefer to see a team made up of people who are born and bred, and so on, but I think we have to play within the rules and get the very best team. I think that's what the public want; I think that's what the fans want."
Asked if the five-year residency rule was sufficient a qualification, Bernstein added: "If that is the rule and we can take advantage of the rule then I think probably we should if that gives us a better team."
Bernstein, who stepped down this year after turning 70, to be succeeded by Greg Dyke, presented a view that was starkly different to 21-year-old Wilshere's theory.
Arsenal man Wilshere, born in Stevenage, said: "The only people who should play for England are English people.
"If you live in England for five years it doesn't make you English. If I went to Spain and lived there for five years I am not going to play for Spain.
"We have to remember what we are. We are English. We tackle hard, are tough on the pitch and are hard to beat.
"We have great characters. You think of Spain and you think technical but you think of England and you think they are brave and they tackle hard. We have to remember that."