The current national flag also made an appearance at the TPP signing, albeit in a less prominent position on the stage behind member countries' trade ministers.
Mr Key has worn a silver fern pin for several years, but rarely at such a high-level occasion.
He has begun wearing the fern emblem more regularly as the March referendum on a national flag approaches.
The Prime Minister has long campaigned for a change of national flag, and has made no secret of his preference for a silver fern design.
New Zealand First leader Winston Peters, who opposes a flag change, said Mr Key was free to wear whatever he wanted.
"However, I don't think portraying himself as a show pony for the new flag option is going to cut any ice with the New Zealand people," he said.
The choice of lapel pin also prompted discussion on social media, with several commenters questioning why the Prime Minister was not wearing New Zealand's official flag at such a major occasion.
Mr Key said last year that he wore the silver fern because "it, to me, symbolises this country that I love and so proudly serve".
He said many New Zealanders, such as All Blacks fans, had already adopted the fern.
In doing so, he said, "they have adopted a symbol that unites them as belonging to a young and proudly independent country that has achieved a lot and has more to do".
