An email sent by a club official on Wednesday was accidentally circulated to the AFL national media list, which numbers more than 1000 and includes accredited football media and key officials from every AFL club.
The email mentioned concerns from Wood, and at least one other club, about the Power’s planned junior programs.
Each of the Port Adelaide’s non-selected AFL players will play for the Magpies in the SANFL next year and an academy team for 18 to 22-year-olds will play in the SANFL reserves.
From 2015 onwards the club's current junior structures will be abolished and replaced by several underage development academies.
The email said another club, thought to be Adelaide, had raised concerns about the programs.
AFL rules dictate that no club is allowed to coach players under 18 years of age.
Thomas insisted all was above board.
"I'd already had a conversation with Ken (Wood) and all we were doing was flagging the language we used in that memo more than anything else," Thomas said.
"What they [the AFL] don't want is a club having access to underage players and hiding them inside the system.
"That's not our intention at all.
"Any additional academy pathways that you create just need to go through them to make sure that we're not breaching any of their regulations.
"We have no issues at all - I guarantee you."
Thomas said there would be no coaching influence from senior Port Adelaide staff on its underage players.
As for next season's reserves coach, Thomas said Ken Hinkley would be consulted once the club's AFL finals campaign ended.
"The whole coaching structure will be integrated, Ken McGregor (current Magpies coach) is in that mix as are all the coaches," he said.
"How it plays out, I'm not sure yet. We'll do that once the season's finished."
