The Manchester United youngster could eventually be eligible for England through residency, but the Arsenal midfielder appeared to raise concerns about the 18-year-old being called into the squad in the future.
"The only people who should play for England are English people," he said at an England press conference on Tuesday ahead of their World Cup qualifiers against Montenegro and Poland.
"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."
Wilshere has since suggested that some of his comments were taken out of context.
He wrote on Twitter: "Just to clarify a few things....again!
"Seems to be a trend in this country, poor journalism in my eyes! I wasn't referring to Januzaj."
"The question was should foreign players be allowed to play for England, and in my opinion I don't think they should! He is a great player...
"I wish he was English! I'm sure most of you agree with me even if some journalist are trying to make me look bad....again!"
Januzaj has never expressed a desire to represent England and is likely to opt for Belgium, the country of his birth.
When asked about whether foreign players should be allowed to play for England, Wilshere had replied: "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."
The situation with players is not clear cut though. There have been plenty of non-English born players who have worn the Three Lions, whilst of the present Under-21 squad, Raheem Sterling was born in Jamaica and Wilfried Zaha in Ivory Coast.