But Mr Shearer will keep his foreign affairs spokesmanship.
There is an implicit suggestion that if Mr Shearer again expresses support for the TPP, he will lose his plum role.
Mr Shearer told the New Zealand Herald on Wednesday that he still supported the TPP - the day after the caucus retreat in Wairarapa decided to oppose the TPP.
"I have spoken with David and he has agreed his comments were careless and did not represent the decision made by the caucus," Mr Little said.
"I instructed him to apologise to his colleagues and he has done so.
"He has assured me that he will now abide by the caucus position."
Mr Little said he believed Mr Shearer would make a "fantastic" foreign affairs minister "and I want to see him in that role".
"However every caucus member knows collective responsibility is a requirement of the party."
Mr Shearer made his comment to the New Zealand Herald the same night that Mr Goff gave an extensive interview on the TPP, and dismissing many of the concerns held by Labour.
But Mr Little said he gave Mr Goff approval to oppose the TPP because he was a former Trade Minister who helped begin TPP.
Both Mr Shearer and Mr Goff are former Labour leaders.
Mr Little and Mr Shearer spoke yesterday and again today and Mr Shearer personally expressed his remorse for having caused disruption.
Mr Little said he accepted his remorse.
Mr Shearer has since emailed colleagues with an apology.
The TPP issue caused heated debate at the caucus retreat. Several other MPs are thought to support the TPP but have maintained caucus discipline.
While Mr Goff has been given permission to support the TPP, he is unlikely to again spell out the reasons for it.
The deal will be signed in Auckland next week.
National seized upon their comments and said Labour's opposition to the TPP showed it was not responsible enough for Government.
ExportNZ today expressed concern that the consensus between the main political parties on trade could be over.
"Previously New Zealand exporters could rely on the support of both main parties on trade," said ExportNZ Executive Director Catherine Beard.
"This has helped our exporters succeed in new markets and earn valuable revenue for New Zealand.
"Exporters are now feeling some dismay at the thought that our future trade prospects could be limited by political disagreement.
It was hard to see why Labour supported the China free trade agreement, but not the TPP when they were similar in all major respects.
"Labour's position on the TPP is a step back for New Zealand's export competitiveness."
