The Irish Football Association has confirmed that Northern Ireland players are requested to have a British passport when playing abroad.
Mr Ahern said issue was laid down in the Good Friday Agreement
The issue has been raised with the European soccer authorities by Irish Foreign Minister Dermot Ahern.
Mr Ahern said players should be allowed to use a British or an Irish passport.
However, the chief executive of the IFA, Howard Wells, said having British papers made life simpler for Northern Ireland teams playing away from home.
"There is not a problem about players travelling on either passport," he said.
"The issue has been that historically, on the administration of some matches that we have had at international level, there has been confusion in the minds of some Uefa officials about the fact... that some of our players have different passports to each other.
"It is because people don't understand the differences, or the uniqueness of Northern Ireland, in terms of our passport issue."
Mr Ahern said: "We have written to Uefa asking them to clarify the position, but also pointing out to them the whole issue that was laid down in the Good Friday Agreement.
"People born after a certain time on the entire island of Ireland can have British or Irish passports - or indeed both.
"There are some people who wish to produce their Irish passport in this respect."