Flower, who toured Pakistan three times with Zimbabwe, explained his stance to the Herald.
"I've been in contact with a number of players and boards around the world to find out whether they [the players] were going to be released.
"New Zealand Cricket's initial stance was that contracted players were not going to be released."
The Herald asked Flower whether Neesham had been in contention.
"We were looking at a number of top players. Jimmy was one of them but, at the time of us making our final selections, as a contracted player he wasn't available so we couldn't select him."
Sources told the Herald that Neesham's application for a NOC had been with NZC for three weeks.
Players can be denied a NOC on the basis of player welfare, as happened when Ross Taylor wanted to play for the Melbourne Renegades in the Big Bash League on New Year's Day too soon after his last game for Central Districts.
Alternatively, an NOC can be withheld if there are injury concerns, or if national duty intervenes.
Neesham is not believed to have contravened any of those conditions.
NZC chief executive David White said permission for any player to attend the series was approved at yesterday's board meeting.
"The board agreed to release both contracted and non-contracted players for that Pakistan series because there's no clash with New Zealand cricket commitments."
Neesham and his management were not available for comment.
Elliott's decision to play is expected to come with a disclaimer that the International Cricket Council will shoulder no liability for his travel, such as insurance costs.
The Pakistan government has promised presidential-level security for the tour. An ICC security unit is expected to visit Lahore this weekend as part of the vetting procedure. The Pakistan Cricket Board is covering all tour expenses.
The World XI matches mark the third time international players have visited Pakistan since the March 2009 terrorist attack on the Sri Lankan team bus.
Zimbabwe embarked on a limited overs tour in May 2015, and the final of the Pakistan Super League was held at Lahore in March. A number of contracted overseas players, including Quetta Gladiator Nathan McCullum, opted out.
New Zealand's last tour to Pakistan was when the Chris Cairns-led one-day international side lost 5-0 in December 2003. A bomb in Karachi ended the May 2002 test tour.
The three T20s will be for the Independence Cup under lights at Gaddafi Stadium on September 12, 13 and 15.
The World XI squad: Faf du Plessis (South Africa, captain), Hashim Amla (South Africa), Samuel Badree (West Indies), George Bailey (Australia), Paul Collingwood (England), Ben Cutting (Australia), Grant Elliott (New Zealand), Tamim Iqbal (Bangladesh), David Miller (South Africa), Morne Morkel (South Africa), Tim Paine (Australia), Thisara Perera (Sri Lanka), Imran Tahir (South Africa), Darren Sammy (West Indies).