The 30-year-old was unavailable for New Zealand's matches against Australia and South Africa in February, but scored 180 not out on his return in the fourth one-day international against the Proteas in Hamilton on March 1.
He will miss the rest of New Zealand's domestic first-class season and the beginning of the Indian Premier League.
"At the moment Martin isn't fit to play and the time we give him now to strengthen his hamstrings will play a big role in mitigating future risk too," New Zealand team physiotherapist Tommy Simsek said in a statement.
"We've put a programme in place to make sure that Martin can return to full strength and we'll continue to monitor him closely."
Coach Mike Hesson said Guptill's importance to the one-day squad for June's Champions Trophy in England meant a complete break from cricket was the best option.
"Having Martin fully fit is critical, as we all know the positive influence he has on our side," Hesson said.
"Martin knows this is an important period to get back to 100 percent so that he can be fully confident when he is on the park.
"The Champions Trophy isn't far away and we obviously want Martin firing on all cylinders for that tournament."
(Reporting by Greg Stutchbury; Editing by Nick Mulvenney)
