The Blackcaps head to the United Arab Emirates in October to play a series of Tests, one-day internationals and Twenty20 matches against Pakistan, and Pakistan had asked if they could host at least the T20s on home soil.
But NZC chairman Greg Barclay said "we just decided circumstances weren't right for us to tour at the moment".
"At the end of the day it came down to following the (government) advisory and the security reports we'd obtained," he added.
"There's no doubt they (Pakistan) are disappointed. I think they saw a tour by a country like New Zealand as being a great precedent for them to start to build an international programme back in Pakistan."
New Zealand's last visit to Pakistan was in 2003, after their tour the previous year abruptly ended when a bomb exploded outside their hotel on the morning the second Test was due to begin in Karachi.
Following a 2009 terrorist attack on Sri Lanka's team in Lahore, Pakistan have played most of their home games in the United Arab Emirates.
Barclay said New Zealand were "very sympathetic" to their plight but "given the current circumstances, it just wasn't right for us to accept the invitation to play in Pakistan".
Four months ago, West Indies became the first side to tour Pakistan in nine years when they played three incident-free matches there.
First Published: August 1, 2018, 9:51 AM IST