Southee suffered a foot injury during the third One-Day International against Sri Lanka in Nelson which forced him to miss the remaining two games of the series.
He also missed the two-match T20I series against Sri Lanka after failing to make a satisfying recovery.
Just when the 27-year-old was aiming to make a comeback for the T20I series against Pakistan, the CT scan on his foot showed more bruising forcing him to miss the action.
New Zealand batting coach Craig McMillan stated that Southee is now targeting a comeback for the ODI series against Australia which begins on 3rd February.
"It's something that will take a wee while to get right," said McMillan to radio station Newstalk ZB.
"I'm not exactly sure of the time frame - whether it's two to three weeks - as to where he is at.
"The plan in place, fingers crossed, is that hopefully he'll be back for the end of the season - back firing for the Australia series."
In the absence of Southee, Trent Boult led the bowling alongside Matt Henry and Adam Milne in the second T20I against Sri Lanka in Auckland, which the Black Caps won convincingly by nine wickets.
© Cricket World 2016