Taylor was stripped of the one-day and Twenty20 captaincy last week at the recommendation of head coach Mike Hesson after the tour of Sri Lanka and the disgruntled batsman turned down the offer to continue as test skipper.
Brendon McCullum was named the new captain in all three formats while Taylor opted out of the team's tour of South Africa.
"The board has reviewed all aspects of the captaincy issue and wishes to publicly place on record its apologies to Ross Taylor and his family for the manner in which events have unfolded," NZC chairman Chris Moller told reporters in Wellington, reading from a prepared statement.
Former players and pundits have slammed NZC for the captaincy controversy and said the episode had made Hesson's job untenable but Moller said no heads would roll.
"There are no hanging offences in all of this," he said.
"Yes, the ball's been dropped, absolutely. Could we have done things better? Absolutely. Are we going to learn from those mistakes, well we hope so."
Taylor, New Zealand's top test batsman, acknowledged the apology in a post on his Twitter account.
"I appreciate the apology from NZC today," he tweeted. "Keen to put it behind me and looking forward to getting back with the team soon."
New Zealand head to South Africa this month to play three Twenty20 internationals before the first of a two-test series against the Proteas gets underway in Cape Town on Jan. 2. (Reporting by Ian Ransom in Melbourne and Sudipto Ganguly in Mumbai; Editing by Amlan Chakraborty)