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The Kiwis were scheduled to fly out of Islamabad Airport at 6pm local time (1am Sunday NZT), and their flight departed after a small delay.
A total of 33 in the tour party, including 21 players, received a full police escort to the airport on bulletproof buses, four hours before their scheduled departure.
"A chartered flight came from the United Arab Emirates to collect the New Zealand squad," a Pakistani official told AFP on Saturday.
'Had to be taken seriously'
The New Zealand government remains steadfast in its support of New Zealand Cricket's last-minute decision to abandon the Black Caps' tour of Pakistan, despite stinging criticism from Pakistan authorities and the wider cricket community.
NZC made the call to cancel the tour just minutes before the first ODI in Rawalpindi on Friday night, following intelligence of a security threat targeting the Black Caps.
All 15 squad members, who trained under heavy police guard three times since their arrival a week ago, were ordered to remain in their hotel rooms - and will now be rushed out of the country.
According to overseas media, the intelligence came from Five Eyes, an intelligence alliance of New Zealand, Australia, Canada, the United States and United Kingdom. The threat was deemed credible before the match, and led to phone calls between NZC and their counterparts at the Pakistan Cricket Board, and Pakistan and New Zealand Prime Ministers Imran Khan and Jacinda Ardern.
Within 12 hours of those conversations, the tour was cancelled.
New Zealand had not toured Pakistan since 2003, due to long-held security concerns after a 2002 suicide bomb attack outside their Karachi hotel, while in 2009, the Sri Lanka team's bus was attacked in Lahore.
In the aftermath of the cancellation, Pakistan media reported the existence of a Rawalpindi police advisory that cited a threat to the tour, issued earlier this week.
New Zealand Deputy Prime Minister Grant Robertson would not confirm whether that was the threat that caused the tour to be abandoned, but noted the threat was credible and action needed to be taken.
"As is normal in situations like this it is not possible or responsible to go into detail around the nature of these threats, but it was credible and had to be taken seriously.
"We support the decision made by NZ Cricket. They did so on the basis of security assessments, including by their own security advisors on the ground. There was a credible security threat and NZ Cricket has responded appropriately.
"We are grateful to the government of Pakistan for keeping the team safe while they have been there, and appreciate how disappointing this decision is for the cricket community in Pakistan. However, player safety has to be paramount. We continue to work closely with NZ Cricket to support them and the players."
The decision left the Pakistan government and cricket community in shock, with one official claiming that Ardern had told Khan that she feared the Black Caps would be attacked once they arrived at the stadium for the first ODI.
Pakistan's Interior Minister Sheikh Rashid Ahmed also echoed earlier comments from the PCB that there was no security threat against the Kiwis.
"He [Khan] told her [Ardern] that the law and order situation is the best in our country and we give a guarantee that there is no security problem here, there is no security threat," Ahmed said.
"But the Prime Minister of New Zealand said that the issue is not the threat but we have such information that when the team goes out it can come under some attack."
According to Ahmed, Black Caps security advised local authorities of the security threat on Friday. When asked about the nature of the threat, Ahmed claimed the New Zealanders "did not have any".
Pakistan had deployed commandos from Pakistan Army's Special Services Group, soldiers, and 4000 policemen for the matches in Rawalpindi, Ahmed said.
He also claimed the cancellation was a "conspiracy", but declined to elaborate.
"He [Khan] called [Ardern] and assured her of complete security to the Kiwis.
"She said the [New Zealand] Government received intelligence that the team could be attacked when it steps out to go to the stadium.
"It is their decision. We had deployed heavy security for the team. Pakistan is a peace promoter in the world. And this tour was cancelled through a conspiracy. It is their problem and what they decide."
The New Zealand women's team, the White Ferns, are scheduled to visit Pakistan this season, and the men's side are also supposed to visit again in 2022-23, for a series of tests and ODIs.
The Black Caps' next matches are set to be at the Twenty20 World Cup, which begins in the United Arab Emirates at the end of October. Their first opponent will be Pakistan.